diff --git a/cli/cli_progress.go b/cli/cli_progress.go
index 5c8657baa..7dcaafbdb 100644
--- a/cli/cli_progress.go
+++ b/cli/cli_progress.go
@@ -89,24 +89,6 @@ func (p *cliProgress) CachedFile(fname string, numBytes int64) {
 	p.maybeOutput()
 }
 
-func (p *cliProgress) Checkpoint() {
-	p.output(noticeColor, "Saving a checkpoint...\n")
-
-	if p.shared {
-		// do not reset counters
-		return
-	}
-
-	*p = cliProgress{
-		uploading:         1,
-		uploadStartTime:   clock.Now(),
-		previousFileCount: p.previousFileCount,
-		previousTotalSize: p.previousTotalSize,
-		uploadedBytes:     p.uploadedBytes,
-		uploadedFiles:     p.uploadedFiles,
-	}
-}
-
 func (p *cliProgress) maybeOutput() {
 	if atomic.LoadInt32(&p.uploading) == 0 {
 		return
diff --git a/fs/entry.go b/fs/entry.go
index cbf21d748..b6bdcbbbf 100644
--- a/fs/entry.go
+++ b/fs/entry.go
@@ -89,6 +89,15 @@ type DirectorySummary struct {
 	FailedEntries []*EntryWithError `json:"errors,omitempty"`
 }
 
+// Clone clones given directory summary.
+func (s *DirectorySummary) Clone() DirectorySummary {
+	res := *s
+
+	res.FailedEntries = append([]*EntryWithError(nil), s.FailedEntries...)
+
+	return res
+}
+
 // Symlink represents a symbolic link entry.
 type Symlink interface {
 	Entry
diff --git a/repo/object/object_manager_test.go b/repo/object/object_manager_test.go
index 467841871..0baca9cd8 100644
--- a/repo/object/object_manager_test.go
+++ b/repo/object/object_manager_test.go
@@ -148,6 +148,78 @@ func TestWriterCompleteChunkInTwoWrites(t *testing.T) {
 	}
 }
 
+func TestCheckpointing(t *testing.T) {
+	ctx := testlogging.Context(t)
+	_, om := setupTest(t)
+
+	writer := om.NewWriter(ctx, WriterOptions{})
+
+	// write all zeroes
+	allZeroes := make([]byte, 1<<20)
+
+	// empty file, nothing flushed
+	checkpoint1, err := writer.Checkpoint()
+	verifyNoError(t, err)
+
+	// write some bytes, but not enough to flush.
+	writer.Write(allZeroes[0:50])
+	checkpoint2, err := writer.Checkpoint()
+	verifyNoError(t, err)
+
+	// write enough to flush first content.
+	writer.Write(allZeroes)
+	checkpoint3, err := writer.Checkpoint()
+	verifyNoError(t, err)
+
+	// write enough to flush second content.
+	writer.Write(allZeroes)
+	checkpoint4, err := writer.Checkpoint()
+	verifyNoError(t, err)
+
+	result, err := writer.Result()
+	verifyNoError(t, err)
+
+	if !objectIDsEqual(checkpoint1, "") {
+		t.Errorf("unexpected checkpoint1: %v err: %v", checkpoint1, err)
+	}
+
+	if !objectIDsEqual(checkpoint2, "") {
+		t.Errorf("unexpected checkpoint2: %v err: %v", checkpoint2, err)
+	}
+
+	verifyFull(ctx, t, om, checkpoint3, allZeroes)
+	verifyFull(ctx, t, om, checkpoint4, make([]byte, 2<<20))
+	verifyFull(ctx, t, om, result, make([]byte, 2<<20+50))
+}
+
+func verifyFull(ctx context.Context, t *testing.T, om *Manager, oid ID, want []byte) {
+	t.Helper()
+
+	r, err := om.Open(ctx, oid)
+	if err != nil {
+		t.Fatalf("unable to open %v: %v", oid, err)
+	}
+
+	defer r.Close()
+
+	data, err := ioutil.ReadAll(r)
+	if err != nil {
+		t.Fatalf("unable to read all: %v", err)
+	}
+
+	if !bytes.Equal(data, want) {
+		t.Fatalf("unexpected data read for %v", oid)
+	}
+}
+
+func verifyNoError(t *testing.T, err error) {
+	t.Helper()
+
+	if err != nil {
+		t.Fatal(err)
+	}
+}
+
 func verifyIndirectBlock(ctx context.Context, t *testing.T, r *Manager, oid ID) {
 	for indexContentID, isIndirect := oid.IndexObjectID(); isIndirect; indexContentID, isIndirect = indexContentID.IndexObjectID() {
 		if c, _, ok := indexContentID.ContentID(); ok {
diff --git a/repo/object/object_writer.go b/repo/object/object_writer.go
index 9b04c7a4f..313bc6f25 100644
--- a/repo/object/object_writer.go
+++ b/repo/object/object_writer.go
@@ -25,6 +25,12 @@
 type Writer interface {
 	io.WriteCloser
 
+	// Checkpoint returns ID of an object consisting of all contents written to storage so far.
+	// This may not include some data buffered in the writer.
+	// In case nothing has been written yet, returns empty object ID.
+	Checkpoint() (ID, error)
+
+	// Result returns object ID representing all bytes written to the writer.
 	Result() (ID, error)
 }
 
@@ -77,6 +83,8 @@ type objectWriter struct {
 
 	splitter splitter.Splitter
 
+	writeMutex sync.Mutex
+
 	asyncWritesSemaphore chan struct{} // async writes semaphore or  nil
 	asyncWritesWG        sync.WaitGroup
 
@@ -103,6 +111,9 @@ func (w *objectWriter) Close() error {
 }
 
 func (w *objectWriter) Write(data []byte) (n int, err error) {
+	w.writeMutex.Lock()
+	defer w.writeMutex.Unlock()
+
 	dataLen := len(data)
 	w.totalLength += int64(dataLen)
 
@@ -229,6 +240,17 @@ func maybeCompressedContentBytes(comp compression.Compressor, output *bytes.Buff
 	return input, false, nil
 }
 
+func (w *objectWriter) drainWrites() {
+	w.writeMutex.Lock()
+
+	// wait for any in-flight asynchronous writes to finish
+	w.asyncWritesWG.Wait()
+}
+
+func (w *objectWriter) undrainWrites() {
+	w.writeMutex.Unlock()
+}
+
 func (w *objectWriter) Result() (ID, error) {
 	// no need to hold a lock on w.indirectIndexGrowMutex, since growing index only happens synchronously
 	// and never in parallel with calling Result()
@@ -238,13 +260,23 @@ func (w *objectWriter) Result() (ID, error) {
 		}
 	}
 
-	// wait for any asynchronous writes to complete.
-	w.asyncWritesWG.Wait()
+	return w.Checkpoint()
+}
+
+// Checkpoint returns object ID which represents portion of the object that has already been written.
+// The result may be an empty object ID if nothing has been flushed yet.
+func (w *objectWriter) Checkpoint() (ID, error) {
+	w.drainWrites()
+	defer w.undrainWrites()
 
 	if w.contentWriteError != nil {
 		return "", w.contentWriteError
 	}
 
+	if len(w.indirectIndex) == 0 {
+		return "", nil
+	}
+
 	if len(w.indirectIndex) == 1 {
 		return w.indirectIndex[0].Object, nil
 	}
diff --git a/snapshot/snapshotfs/checkpoint_registry.go b/snapshot/snapshotfs/checkpoint_registry.go
new file mode 100644
index 000000000..2164545ac
--- /dev/null
+++ b/snapshot/snapshotfs/checkpoint_registry.go
@@ -0,0 +1,62 @@
+package snapshotfs
+
+import (
+	"sync"
+
+	"github.com/google/uuid"
+	"github.com/pkg/errors"
+
+	"github.com/kopia/kopia/fs"
+	"github.com/kopia/kopia/snapshot"
+)
+
+// checkpointFunc is invoked when checkpoint occurs. The callback must checkpoint current state of
+// file or directory and return directory entry.
+type checkpointFunc func() (*snapshot.DirEntry, error)
+
+type checkpointRegistry struct {
+	mu sync.Mutex
+
+	checkpoints map[string]checkpointFunc
+}
+
+func (r *checkpointRegistry) addCheckpointCallback(e fs.Entry, f checkpointFunc) {
+	r.mu.Lock()
+	defer r.mu.Unlock()
+
+	if r.checkpoints == nil {
+		r.checkpoints = map[string]checkpointFunc{}
+	}
+
+	r.checkpoints[e.Name()] = f
+}
+
+func (r *checkpointRegistry) removeCheckpointCallback(e fs.Entry) {
+	r.mu.Lock()
+	defer r.mu.Unlock()
+
+	delete(r.checkpoints, e.Name())
+}
+
+// runCheckpoints invokes all registered checkpointers and adds results to the provided builder, while
+// randomizing file names for non-directory entries. this is to prevent the use of checkpointed objects
+// as authoritative on subsequent runs.
+func (r *checkpointRegistry) runCheckpoints(checkpointBuilder *dirManifestBuilder) error {
+	r.mu.Lock()
+	defer r.mu.Unlock()
+
+	for n, cp := range r.checkpoints {
+		de, err := cp()
+		if err != nil {
+			return errors.Wrapf(err, "error checkpointing %v", n)
+		}
+
+		if de.Type != snapshot.EntryTypeDirectory {
+			de.Name = ".checkpointed." + de.Name + "." + uuid.New().String()
+		}
+
+		checkpointBuilder.addEntry(de)
+	}
+
+	return nil
+}
diff --git a/snapshot/snapshotfs/checkpoint_registry_test.go b/snapshot/snapshotfs/checkpoint_registry_test.go
new file mode 100644
index 000000000..f3e79af81
--- /dev/null
+++ b/snapshot/snapshotfs/checkpoint_registry_test.go
@@ -0,0 +1,82 @@
+package snapshotfs
+
+import (
+	"os"
+	"strings"
+	"testing"
+
+	"github.com/kopia/kopia/internal/clock"
+	"github.com/kopia/kopia/internal/mockfs"
+	"github.com/kopia/kopia/snapshot"
+)
+
+func TestCheckpointRegistry(t *testing.T) {
+	var cp checkpointRegistry
+
+	d := mockfs.NewDirectory()
+	dir1 := d.AddDir("dir1", os.FileMode(0o755))
+	f1 := d.AddFile("f1", []byte{1, 2, 3}, os.FileMode(0o755))
+	f2 := d.AddFile("f2", []byte{2, 3, 4}, os.FileMode(0o755))
+	f3 := d.AddFile("f3", []byte{2, 3, 4}, os.FileMode(0o755))
+
+	cp.addCheckpointCallback(dir1, func() (*snapshot.DirEntry, error) {
+		return &snapshot.DirEntry{
+			Name: "dir1",
+			Type: snapshot.EntryTypeDirectory,
+		}, nil
+	})
+
+	cp.addCheckpointCallback(f1, func() (*snapshot.DirEntry, error) {
+		return &snapshot.DirEntry{
+			Name: "f1",
+		}, nil
+	})
+
+	cp.addCheckpointCallback(f2, func() (*snapshot.DirEntry, error) {
+		return &snapshot.DirEntry{
+			Name: "f2",
+		}, nil
+	})
+
+	cp.addCheckpointCallback(f3, func() (*snapshot.DirEntry, error) {
+		return &snapshot.DirEntry{
+			Name: "other",
+		}, nil
+	})
+
+	// remove callback before it has a chance of firing
+	cp.removeCheckpointCallback(f3)
+	cp.removeCheckpointCallback(f3)
+
+	var dmb dirManifestBuilder
+
+	dmb.addEntry(&snapshot.DirEntry{
+		Name: "pre-existing",
+	})
+
+	if err := cp.runCheckpoints(&dmb); err != nil {
+		t.Fatalf("error running checkpoints: %v", err)
+	}
+
+	dm := dmb.Build(clock.Now(), "checkpoint")
+	if got, want := len(dm.Entries), 4; got != want {
+		t.Fatalf("got %v entries, wanted %v (%+#v)", got, want, dm.Entries)
+	}
+
+	// directory names don't get mangled
+	if dm.Entries[0].Name != "dir1" {
+		t.Errorf("invalid entry %v", dm.Entries[0])
+	}
+
+	if !strings.HasPrefix(dm.Entries[1].Name, ".checkpointed.f1.") {
+		t.Errorf("invalid entry %v", dm.Entries[1])
+	}
+
+	if !strings.HasPrefix(dm.Entries[2].Name, ".checkpointed.f2.") {
+		t.Errorf("invalid entry %v", dm.Entries[2])
+	}
+
+	if dm.Entries[3].Name != "pre-existing" {
+		t.Errorf("invalid entry %v", dm.Entries[3])
+	}
+}
diff --git a/snapshot/snapshotfs/upload.go b/snapshot/snapshotfs/upload.go
index 6bee4b38d..d1f8b5cd1 100644
--- a/snapshot/snapshotfs/upload.go
+++ b/snapshot/snapshotfs/upload.go
@@ -69,11 +69,15 @@ type Uploader struct {
 
 	repo repo.Repository
 
-	stats              snapshot.Stats
-	canceled           int32
-	nextCheckpointTime time.Time
+	stats    snapshot.Stats
+	canceled int32
 
 	uploadBufPool sync.Pool
+
+	getTicker func(time.Duration) <-chan time.Time
+
+	// for testing only, when set will write to a given channel whenever checkpoint completes
+	checkpointFinished chan struct{}
 }
 
 // IsCanceled returns true if the upload is canceled.
@@ -87,10 +91,6 @@ func (u *Uploader) incompleteReason() string {
 		return IncompleteReasonCanceled
 	}
 
-	if !u.nextCheckpointTime.IsZero() && u.repo.Time().After(u.nextCheckpointTime) {
-		return IncompleteReasonCheckpoint
-	}
-
 	wb := atomic.LoadInt64(&u.totalWrittenBytes)
 	if mub := u.MaxUploadBytes; mub > 0 && wb > mub {
 		return IncompleteReasonLimitReached
@@ -99,7 +99,7 @@ func (u *Uploader) incompleteReason() string {
 	return ""
 }
 
-func (u *Uploader) uploadFileInternal(ctx context.Context, relativePath string, f fs.File, pol *policy.Policy, asyncWrites int) (*snapshot.DirEntry, error) {
+func (u *Uploader) uploadFileInternal(ctx context.Context, parentCheckpointRegistry *checkpointRegistry, relativePath string, f fs.File, pol *policy.Policy, asyncWrites int) (*snapshot.DirEntry, error) {
 	u.Progress.HashingFile(relativePath)
 	defer u.Progress.FinishedHashingFile(relativePath, f.Size())
 
@@ -116,6 +116,18 @@ func (u *Uploader) uploadFileInternal(ctx context.Context, relativePath string,
 	})
 	defer writer.Close() //nolint:errcheck
 
+	parentCheckpointRegistry.addCheckpointCallback(f, func() (*snapshot.DirEntry, error) {
+		// nolint:govet
+		checkpointID, err := writer.Checkpoint()
+		if err != nil {
+			return nil, err
+		}
+
+		return newDirEntry(f, checkpointID)
+	})
+
+	defer parentCheckpointRegistry.removeCheckpointCallback(f)
+
 	written, err := u.copyWithProgress(writer, file, 0, f.Size())
 	if err != nil {
 		return nil, err
@@ -138,6 +150,9 @@ func (u *Uploader) uploadFileInternal(ctx context.Context, relativePath string,
 
 	de.FileSize = written
 
+	atomic.AddInt32(&u.stats.TotalFileCount, 1)
+	atomic.AddInt64(&u.stats.TotalFileSize, de.FileSize)
+
 	return de, nil
 }
 
@@ -225,6 +240,17 @@ func (u *Uploader) copyWithProgress(dst io.Writer, src io.Reader, completed, len
 	return written, nil
 }
 
+func newDirEntryWithSummary(d fs.Entry, oid object.ID, summ *fs.DirectorySummary) (*snapshot.DirEntry, error) {
+	de, err := newDirEntry(d, oid)
+	if err != nil {
+		return nil, err
+	}
+
+	de.DirSummary = summ
+
+	return de, nil
+}
+
 func newDirEntry(md fs.Entry, oid object.ID) (*snapshot.DirEntry, error) {
 	var entryType snapshot.EntryType
 
@@ -251,82 +277,113 @@ func newDirEntry(md fs.Entry, oid object.ID) (*snapshot.DirEntry, error) {
 	}, nil
 }
 
-// uploadFile uploads the specified File to the repository.
-func (u *Uploader) uploadFile(ctx context.Context, relativePath string, file fs.File, pol *policy.Policy) (*snapshot.DirEntry, error) {
+// uploadFileWithCheckpointing uploads the specified File to the repository.
+func (u *Uploader) uploadFileWithCheckpointing(ctx context.Context, relativePath string, file fs.File, pol *policy.Policy, sourceInfo snapshot.SourceInfo) (*snapshot.DirEntry, error) {
 	par := u.effectiveParallelUploads()
 	if par == 1 {
 		par = 0
 	}
 
-	res, err := u.uploadFileInternal(ctx, relativePath, file, pol, par)
+	var cp checkpointRegistry
+
+	cancelCheckpointer := u.periodicallyCheckpoint(ctx, &cp, &snapshot.Manifest{Source: sourceInfo})
+	defer cancelCheckpointer()
+
+	res, err := u.uploadFileInternal(ctx, &cp, relativePath, file, pol, par)
 	if err != nil {
 		return nil, err
 	}
 
-	de, err := newDirEntry(file, res.ObjectID)
-	if err != nil {
-		return nil, errors.Wrap(err, "unable to create dir entry")
-	}
-
-	de.DirSummary = &fs.DirectorySummary{
+	return newDirEntryWithSummary(file, res.ObjectID, &fs.DirectorySummary{
 		TotalFileCount: 1,
 		TotalFileSize:  res.FileSize,
 		MaxModTime:     res.ModTime,
+	})
+}
+
+// checkpointRoot invokes checkpoints on the provided registry and if a checkpoint entry was generated,
+// saves it in an incomplete snapshot manifest.
+func (u *Uploader) checkpointRoot(ctx context.Context, cp *checkpointRegistry, prototypeManifest *snapshot.Manifest) error {
+	var dmbCheckpoint dirManifestBuilder
+	if err := cp.runCheckpoints(&dmbCheckpoint); err != nil {
+		return errors.Wrap(err, "running checkpointers")
 	}
 
-	return de, nil
+	checkpointManifest := dmbCheckpoint.Build(u.repo.Time(), "dummy")
+	if len(checkpointManifest.Entries) == 0 {
+		// did not produce a checkpoint, that's ok
+		return nil
+	}
+
+	if len(checkpointManifest.Entries) > 1 {
+		return errors.Errorf("produced more than one checkpoint: %v", len(checkpointManifest.Entries))
+	}
+
+	rootEntry := checkpointManifest.Entries[0]
+
+	log(ctx).Debugf("checkpointed root %v", rootEntry.ObjectID)
+
+	man := *prototypeManifest
+	man.RootEntry = rootEntry
+	man.EndTime = u.repo.Time()
+	man.StartTime = man.EndTime
+	man.IncompleteReason = IncompleteReasonCheckpoint
+
+	if _, err := snapshot.SaveSnapshot(ctx, u.repo, &man); err != nil {
+		return errors.Wrap(err, "error saving checkpoint snapshot")
+	}
+
+	if err := u.repo.Flush(ctx); err != nil {
+		return errors.Wrap(err, "error flushing after checkpoint")
+	}
+
+	return nil
+}
+
+// periodicallyCheckpoint periodically (every CheckpointInterval) invokes checkpointRoot until the
+// returned cancelation function has been called.
+func (u *Uploader) periodicallyCheckpoint(ctx context.Context, cp *checkpointRegistry, prototypeManifest *snapshot.Manifest) (cancelFunc func()) {
+	shutdown := make(chan struct{})
+	ch := u.getTicker(u.CheckpointInterval)
+
+	go func() {
+		for {
+			select {
+			case <-shutdown:
+				return
+
+			case <-ch:
+				if err := u.checkpointRoot(ctx, cp, prototypeManifest); err != nil {
+					log(ctx).Warningf("error checkpointing: %v", err)
+					u.Cancel()
+
+					return
+				}
+
+				// test hook
+				if u.checkpointFinished != nil {
+					u.checkpointFinished <- struct{}{}
+				}
+			}
+		}
+	}()
+
+	return func() {
+		close(shutdown)
+	}
 }
 
 // uploadDirWithCheckpointing uploads the specified Directory to the repository.
 func (u *Uploader) uploadDirWithCheckpointing(ctx context.Context, rootDir fs.Directory, policyTree *policy.Tree, previousDirs []fs.Directory, sourceInfo snapshot.SourceInfo) (*snapshot.DirEntry, error) {
-	for {
-		if u.CheckpointInterval != 0 {
-			u.nextCheckpointTime = u.repo.Time().Add(u.CheckpointInterval)
-		} else {
-			u.nextCheckpointTime = time.Time{}
-		}
+	var (
+		dmb dirManifestBuilder
+		cp  checkpointRegistry
+	)
 
-		startTime := u.repo.Time()
+	cancelCheckpointer := u.periodicallyCheckpoint(ctx, &cp, &snapshot.Manifest{Source: sourceInfo})
+	defer cancelCheckpointer()
 
-		oid, summ, err := uploadDirInternal(ctx, u, rootDir, policyTree, previousDirs, ".")
-		if err != nil && !errors.Is(err, errCanceled) {
-			return nil, err
-		}
-
-		de, err := newDirEntry(rootDir, oid)
-		if err != nil {
-			return nil, errors.Wrap(err, "unable to create dir entry")
-		}
-
-		de.DirSummary = &summ
-
-		if summ.IncompleteReason == IncompleteReasonCheckpoint {
-			u.Progress.Checkpoint()
-
-			// when retrying use the partial snapshot
-			previousDirs = append(previousDirs, DirectoryEntry(u.repo, oid, &summ))
-
-			man := &snapshot.Manifest{
-				StartTime:        startTime,
-				EndTime:          u.repo.Time(),
-				RootEntry:        de,
-				Source:           sourceInfo,
-				IncompleteReason: summ.IncompleteReason,
-			}
-
-			if _, err = snapshot.SaveSnapshot(ctx, u.repo, man); err != nil {
-				return nil, errors.Wrap(err, "error saving checkpoint")
-			}
-
-			if err = u.repo.Flush(ctx); err != nil {
-				return nil, errors.Wrap(err, "error flushing saving checkpoint")
-			}
-
-			continue
-		}
-
-		return de, err
-	}
+	return uploadDirInternal(ctx, u, rootDir, policyTree, previousDirs, ".", &dmb, &cp)
 }
 
 func (u *Uploader) foreachEntryUnlessCanceled(ctx context.Context, parallel int, relativePath string, entries fs.Entries, cb func(ctx context.Context, entry fs.Entry, entryRelativePath string) error) error {
@@ -377,11 +434,6 @@ func (u *Uploader) foreachEntryUnlessCanceled(ctx context.Context, parallel int,
 	return eg.Wait()
 }
 
-type dirEntryOrError struct {
-	de          *snapshot.DirEntry
-	failedEntry *fs.EntryWithError
-}
-
 func rootCauseError(err error) error {
 	err = errors.Cause(err)
 	if oserr, ok := err.(*os.PathError); ok {
@@ -391,106 +443,124 @@ func rootCauseError(err error) error {
 	return err
 }
 
-func (u *Uploader) populateChildEntries(parent *snapshot.DirManifest, children <-chan dirEntryOrError) {
-	parentSummary := parent.Summary
+type dirManifestBuilder struct {
+	mu sync.Mutex
 
-	for it := range children {
-		if it.failedEntry != nil {
-			parentSummary.NumFailed++
-			parentSummary.FailedEntries = append(parentSummary.FailedEntries, it.failedEntry)
+	summary fs.DirectorySummary
+	entries []*snapshot.DirEntry
+}
 
-			continue
+// Clone clones the current state of dirManifestBuilder.
+func (b *dirManifestBuilder) Clone() *dirManifestBuilder {
+	b.mu.Lock()
+	defer b.mu.Unlock()
+
+	return &dirManifestBuilder{
+		summary: b.summary.Clone(),
+		entries: append([]*snapshot.DirEntry(nil), b.entries...),
+	}
+}
+
+func (b *dirManifestBuilder) addEntry(de *snapshot.DirEntry) {
+	b.mu.Lock()
+	defer b.mu.Unlock()
+
+	b.entries = append(b.entries, de)
+
+	// nolint:exhaustive
+	switch de.Type {
+	case snapshot.EntryTypeFile:
+		b.summary.TotalFileCount++
+		b.summary.TotalFileSize += de.FileSize
+
+		if de.ModTime.After(b.summary.MaxModTime) {
+			b.summary.MaxModTime = de.ModTime
 		}
 
-		de := it.de
+	case snapshot.EntryTypeDirectory:
+		if childSummary := de.DirSummary; childSummary != nil {
+			b.summary.TotalFileCount += childSummary.TotalFileCount
+			b.summary.TotalFileSize += childSummary.TotalFileSize
+			b.summary.TotalDirCount += childSummary.TotalDirCount
+			b.summary.NumFailed += childSummary.NumFailed
+			b.summary.FailedEntries = append(b.summary.FailedEntries, childSummary.FailedEntries...)
 
-		// nolint:exhaustive
-		switch de.Type {
-		case snapshot.EntryTypeFile:
-			u.stats.TotalFileCount++
-			u.stats.TotalFileSize += de.FileSize
-			parentSummary.TotalFileCount++
-			parentSummary.TotalFileSize += de.FileSize
-
-			if de.ModTime.After(parentSummary.MaxModTime) {
-				parentSummary.MaxModTime = de.ModTime
-			}
-
-		case snapshot.EntryTypeDirectory:
-			if childSummary := de.DirSummary; childSummary != nil {
-				parentSummary.TotalFileCount += childSummary.TotalFileCount
-				parentSummary.TotalFileSize += childSummary.TotalFileSize
-				parentSummary.TotalDirCount += childSummary.TotalDirCount
-				parentSummary.NumFailed += childSummary.NumFailed
-				parentSummary.FailedEntries = append(parentSummary.FailedEntries, childSummary.FailedEntries...)
-
-				if childSummary.MaxModTime.After(parentSummary.MaxModTime) {
-					parentSummary.MaxModTime = childSummary.MaxModTime
-				}
+			if childSummary.MaxModTime.After(b.summary.MaxModTime) {
+				b.summary.MaxModTime = childSummary.MaxModTime
 			}
 		}
+	}
+}
 
-		parent.Entries = append(parent.Entries, de)
+func (b *dirManifestBuilder) addFailedEntry(relPath string, err error) {
+	b.mu.Lock()
+	defer b.mu.Unlock()
+
+	b.summary.NumFailed++
+	b.summary.FailedEntries = append(b.summary.FailedEntries, &fs.EntryWithError{
+		EntryPath: relPath,
+		Error:     err.Error(),
+	})
+}
+
+func (b *dirManifestBuilder) Build(dirModTime time.Time, incompleteReason string) *snapshot.DirManifest {
+	b.mu.Lock()
+	defer b.mu.Unlock()
+
+	s := b.summary
+	s.TotalDirCount++
+
+	if len(b.entries) == 0 {
+		s.MaxModTime = dirModTime
 	}
 
+	s.IncompleteReason = incompleteReason
+
 	// take top N sorted failed entries
-	if len(parent.Summary.FailedEntries) > 0 {
-		sort.Slice(parent.Summary.FailedEntries, func(i, j int) bool {
-			return parent.Summary.FailedEntries[i].EntryPath < parent.Summary.FailedEntries[j].EntryPath
+	if len(b.summary.FailedEntries) > 0 {
+		sort.Slice(b.summary.FailedEntries, func(i, j int) bool {
+			return b.summary.FailedEntries[i].EntryPath < b.summary.FailedEntries[j].EntryPath
 		})
 
-		if len(parent.Summary.FailedEntries) > fs.MaxFailedEntriesPerDirectorySummary {
-			parent.Summary.FailedEntries = parent.Summary.FailedEntries[0:fs.MaxFailedEntriesPerDirectorySummary]
+		if len(b.summary.FailedEntries) > fs.MaxFailedEntriesPerDirectorySummary {
+			b.summary.FailedEntries = b.summary.FailedEntries[0:fs.MaxFailedEntriesPerDirectorySummary]
 		}
 	}
 
 	// sort the result, directories first, then non-directories, ordered by name
-	sort.Slice(parent.Entries, func(i, j int) bool {
-		if leftDir, rightDir := isDir(parent.Entries[i]), isDir(parent.Entries[j]); leftDir != rightDir {
+	sort.Slice(b.entries, func(i, j int) bool {
+		if leftDir, rightDir := isDir(b.entries[i]), isDir(b.entries[j]); leftDir != rightDir {
 			// directories get sorted before non-directories
 			return leftDir
 		}
 
-		return parent.Entries[i].Name < parent.Entries[j].Name
+		return b.entries[i].Name < b.entries[j].Name
 	})
+
+	return &snapshot.DirManifest{
+		StreamType: directoryStreamType,
+		Summary:    &s,
+		Entries:    b.entries,
+	}
 }
 
 func isDir(e *snapshot.DirEntry) bool {
 	return e.Type == snapshot.EntryTypeDirectory
 }
 
-func (u *Uploader) processChildren(ctx context.Context, dirManifest *snapshot.DirManifest, relativePath string, entries fs.Entries, policyTree *policy.Tree, previousEntries []fs.Entries) error {
-	var wg sync.WaitGroup
-
-	// channel where we will add directory and file entries, possibly in parallel
-	output := make(chan dirEntryOrError)
-
-	// goroutine that will drain data from 'output' and update dirManifest
-	wg.Add(1)
-
-	go func() {
-		defer wg.Done()
-		u.populateChildEntries(dirManifest, output)
-	}()
-
-	defer func() {
-		// before this function returns, close the output channel and wait for the goroutine above to complete.
-		close(output)
-		wg.Wait()
-	}()
-
-	if err := u.processSubdirectories(ctx, output, relativePath, entries, policyTree, previousEntries); err != nil {
+func (u *Uploader) processChildren(ctx context.Context, parentDirCheckpointRegistry *checkpointRegistry, parentDirBuilder *dirManifestBuilder, relativePath string, entries fs.Entries, policyTree *policy.Tree, previousEntries []fs.Entries) error {
+	if err := u.processSubdirectories(ctx, parentDirCheckpointRegistry, parentDirBuilder, relativePath, entries, policyTree, previousEntries); err != nil {
 		return err
 	}
 
-	if err := u.processNonDirectories(ctx, output, relativePath, entries, policyTree, previousEntries); err != nil {
+	if err := u.processNonDirectories(ctx, parentDirCheckpointRegistry, parentDirBuilder, relativePath, entries, policyTree, previousEntries); err != nil {
 		return err
 	}
 
 	return nil
 }
 
-func (u *Uploader) processSubdirectories(ctx context.Context, output chan dirEntryOrError, relativePath string, entries fs.Entries, policyTree *policy.Tree, previousEntries []fs.Entries) error {
+func (u *Uploader) processSubdirectories(ctx context.Context, parentDirCheckpointRegistry *checkpointRegistry, parentDirBuilder *dirManifestBuilder, relativePath string, entries fs.Entries, policyTree *policy.Tree, previousEntries []fs.Entries) error {
 	// for now don't process subdirectories in parallel, we need a mechanism to
 	// prevent explosion of parallelism
 	const parallelism = 1
@@ -511,7 +581,9 @@ func (u *Uploader) processSubdirectories(ctx context.Context, output chan dirEnt
 
 		previousDirs = uniqueDirectories(previousDirs)
 
-		oid, subdirsumm, err := uploadDirInternal(ctx, u, dir, policyTree.Child(entry.Name()), previousDirs, entryRelativePath)
+		childDirBuilder := &dirManifestBuilder{}
+
+		de, err := uploadDirInternal(ctx, u, dir, policyTree.Child(entry.Name()), previousDirs, entryRelativePath, childDirBuilder, parentDirCheckpointRegistry)
 		if errors.Is(err, errCanceled) {
 			return err
 		}
@@ -525,24 +597,15 @@ func (u *Uploader) processSubdirectories(ctx context.Context, output chan dirEnt
 				rc := rootCauseError(dre.error)
 
 				u.Progress.IgnoredError(entryRelativePath, rc)
-				output <- dirEntryOrError{
-					failedEntry: &fs.EntryWithError{
-						EntryPath: entryRelativePath,
-						Error:     rc.Error(),
-					},
-				}
+				parentDirBuilder.addFailedEntry(entryRelativePath, rc)
 				return nil
 			}
+
 			return errors.Errorf("unable to process directory %q: %s", entry.Name(), err)
 		}
 
-		de, err := newDirEntry(dir, oid)
-		if err != nil {
-			return errors.Wrap(err, "unable to create dir entry")
-		}
+		parentDirBuilder.addEntry(de)
 
-		de.DirSummary = &subdirsumm
-		output <- dirEntryOrError{de: de}
 		return nil
 	})
 }
@@ -605,7 +668,7 @@ func (u *Uploader) effectiveParallelUploads() int {
 	return p
 }
 
-func (u *Uploader) processNonDirectories(ctx context.Context, output chan dirEntryOrError, dirRelativePath string, entries fs.Entries, policyTree *policy.Tree, prevEntries []fs.Entries) error {
+func (u *Uploader) processNonDirectories(ctx context.Context, parentCheckpointRegistry *checkpointRegistry, parentDirBuilder *dirManifestBuilder, dirRelativePath string, entries fs.Entries, policyTree *policy.Tree, prevEntries []fs.Entries) error {
 	workerCount := u.effectiveParallelUploads()
 
 	var asyncWritesPerFile int
@@ -639,7 +702,7 @@ func (u *Uploader) processNonDirectories(ctx context.Context, output chan dirEnt
 				return errors.Wrap(err, "unable to create dir entry")
 			}
 
-			output <- dirEntryOrError{de: cachedDirEntry}
+			parentDirBuilder.addEntry(cachedDirEntry)
 			return nil
 		}
 
@@ -647,20 +710,20 @@ func (u *Uploader) processNonDirectories(ctx context.Context, output chan dirEnt
 		case fs.Symlink:
 			de, err := u.uploadSymlinkInternal(ctx, entryRelativePath, entry)
 			if err != nil {
-				return u.maybeIgnoreFileReadError(err, output, entryRelativePath, policyTree)
+				return u.maybeIgnoreFileReadError(err, parentDirBuilder, entryRelativePath, policyTree)
 			}
 
-			output <- dirEntryOrError{de: de}
+			parentDirBuilder.addEntry(de)
 			return nil
 
 		case fs.File:
 			atomic.AddInt32(&u.stats.NonCachedFiles, 1)
-			de, err := u.uploadFileInternal(ctx, entryRelativePath, entry, policyTree.Child(entry.Name()).EffectivePolicy(), asyncWritesPerFile)
+			de, err := u.uploadFileInternal(ctx, parentCheckpointRegistry, entryRelativePath, entry, policyTree.Child(entry.Name()).EffectivePolicy(), asyncWritesPerFile)
 			if err != nil {
-				return u.maybeIgnoreFileReadError(err, output, entryRelativePath, policyTree)
+				return u.maybeIgnoreFileReadError(err, parentDirBuilder, entryRelativePath, policyTree)
 			}
 
-			output <- dirEntryOrError{de: de}
+			parentDirBuilder.addEntry(de)
 			return nil
 
 		default:
@@ -717,25 +780,20 @@ func uploadDirInternal(
 	policyTree *policy.Tree,
 	previousDirs []fs.Directory,
 	dirRelativePath string,
-) (object.ID, fs.DirectorySummary, error) {
+	thisDirBuilder *dirManifestBuilder,
+	thisCheckpointRegistry *checkpointRegistry,
+) (*snapshot.DirEntry, error) {
 	u.stats.TotalDirectoryCount++
 
 	u.Progress.StartedDirectory(dirRelativePath)
 	defer u.Progress.FinishedDirectory(dirRelativePath)
 
-	dirManifest := &snapshot.DirManifest{
-		StreamType: directoryStreamType,
-		Summary: &fs.DirectorySummary{
-			TotalDirCount: 1,
-		},
-	}
-
 	t0 := u.repo.Time()
 	entries, direrr := directory.Readdir(ctx)
 	log(ctx).Debugf("finished reading directory %v in %v", dirRelativePath, u.repo.Time().Sub(t0))
 
 	if direrr != nil {
-		return "", fs.DirectorySummary{}, dirReadError{direrr}
+		return nil, dirReadError{direrr}
 	}
 
 	var prevEntries []fs.Entries
@@ -746,16 +804,43 @@ func uploadDirInternal(
 		}
 	}
 
-	if err := u.processChildren(ctx, dirManifest, dirRelativePath, entries, policyTree, prevEntries); err != nil && !errors.Is(err, errCanceled) {
-		return "", fs.DirectorySummary{}, err
+	childCheckpointRegistry := &checkpointRegistry{}
+
+	thisCheckpointRegistry.addCheckpointCallback(directory, func() (*snapshot.DirEntry, error) {
+		// when snapshotting the parent, snapshot all our children and tell them to populate
+		// childCheckpointBuilder
+		thisCheckpointBuilder := thisDirBuilder.Clone()
+
+		// invoke all child checkpoints which will populate thisCheckpointBuilder.
+		if err := childCheckpointRegistry.runCheckpoints(thisCheckpointBuilder); err != nil {
+			return nil, errors.Wrapf(err, "error checkpointing children")
+		}
+
+		checkpointManifest := thisCheckpointBuilder.Build(directory.ModTime(), IncompleteReasonCheckpoint)
+		oid, err := u.writeDirManifest(ctx, dirRelativePath, checkpointManifest)
+		if err != nil {
+			return nil, errors.Wrap(err, "error writing dir manifest")
+		}
+
+		return newDirEntryWithSummary(directory, oid, checkpointManifest.Summary)
+	})
+	defer thisCheckpointRegistry.removeCheckpointCallback(directory)
+
+	if err := u.processChildren(ctx, childCheckpointRegistry, thisDirBuilder, dirRelativePath, entries, policyTree, prevEntries); err != nil && !errors.Is(err, errCanceled) {
+		return nil, err
 	}
 
-	if len(dirManifest.Entries) == 0 {
-		dirManifest.Summary.MaxModTime = directory.ModTime()
+	dirManifest := thisDirBuilder.Build(directory.ModTime(), u.incompleteReason())
+
+	oid, err := u.writeDirManifest(ctx, dirRelativePath, dirManifest)
+	if err != nil {
+		return nil, errors.Wrapf(err, "error writing dir manifest: %v", directory.Name())
 	}
 
-	// at this point dirManifest is ready to go
+	return newDirEntryWithSummary(directory, oid, dirManifest.Summary)
+}
 
+func (u *Uploader) writeDirManifest(ctx context.Context, dirRelativePath string, dirManifest *snapshot.DirManifest) (object.ID, error) {
 	writer := u.repo.NewObjectWriter(ctx, object.WriterOptions{
 		Description: "DIR:" + dirRelativePath,
 		Prefix:      "k",
@@ -764,26 +849,24 @@ func uploadDirInternal(
 	defer writer.Close() //nolint:errcheck
 
 	if err := json.NewEncoder(writer).Encode(dirManifest); err != nil {
-		return "", fs.DirectorySummary{}, errors.Wrap(err, "unable to encode directory JSON")
+		return "", errors.Wrap(err, "unable to encode directory JSON")
 	}
 
 	oid, err := writer.Result()
+	if err != nil {
+		return "", errors.Wrap(err, "unable to write directory")
+	}
 
-	dirManifest.Summary.IncompleteReason = u.incompleteReason()
-
-	return oid, *dirManifest.Summary, err
+	return oid, nil
 }
 
-func (u *Uploader) maybeIgnoreFileReadError(err error, output chan dirEntryOrError, entryRelativePath string, policyTree *policy.Tree) error {
+func (u *Uploader) maybeIgnoreFileReadError(err error, dmb *dirManifestBuilder, entryRelativePath string, policyTree *policy.Tree) error {
 	errHandlingPolicy := policyTree.EffectivePolicy().ErrorHandlingPolicy
 
 	if u.IgnoreReadErrors || errHandlingPolicy.IgnoreFileErrorsOrDefault(false) {
 		err = rootCauseError(err)
 		u.Progress.IgnoredError(entryRelativePath, err)
-		output <- dirEntryOrError{failedEntry: &fs.EntryWithError{
-			EntryPath: entryRelativePath,
-			Error:     err.Error(),
-		}}
+		dmb.addFailedEntry(entryRelativePath, err)
 
 		return nil
 	}
@@ -809,6 +892,7 @@ func NewUploader(r repo.Repository) *Uploader {
 		IgnoreReadErrors:   false,
 		ParallelUploads:    1,
 		CheckpointInterval: DefaultCheckpointInterval,
+		getTicker:          time.Tick,
 		uploadBufPool: sync.Pool{
 			New: func() interface{} {
 				p := make([]byte, copyBufferSize)
@@ -867,7 +951,7 @@ func (u *Uploader) Upload(
 			maxPreviousTotalFileSize = s
 		}
 
-		if s := m.Stats.TotalFileCount; s > maxPreviousFileCount {
+		if s := int(m.Stats.TotalFileCount); s > maxPreviousFileCount {
 			maxPreviousFileCount = s
 		}
 	}
@@ -898,7 +982,7 @@ func (u *Uploader) Upload(
 		s.RootEntry, err = u.uploadDirWithCheckpointing(ctx, entry, policyTree, previousDirs, sourceInfo)
 
 	case fs.File:
-		s.RootEntry, err = u.uploadFile(ctx, entry.Name(), entry, policyTree.EffectivePolicy())
+		s.RootEntry, err = u.uploadFileWithCheckpointing(ctx, entry.Name(), entry, policyTree.EffectivePolicy(), sourceInfo)
 
 	default:
 		return nil, errors.Errorf("unsupported source: %v", s.Source)
diff --git a/snapshot/snapshotfs/upload_progress.go b/snapshot/snapshotfs/upload_progress.go
index 57213cc1c..6cc8cb1dc 100644
--- a/snapshot/snapshotfs/upload_progress.go
+++ b/snapshot/snapshotfs/upload_progress.go
@@ -36,9 +36,6 @@ type UploadProgress interface {
 
 	// FinishedDirectory is emitted whenever a directory is finished uploading.
 	FinishedDirectory(dirname string)
-
-	// Checkpoint is emitted whenever snapshot is checkpointed.
-	Checkpoint()
 }
 
 // NullUploadProgress is an implementation of UploadProgress that does not produce any output.
@@ -75,9 +72,6 @@ func (p *NullUploadProgress) FinishedDirectory(dirname string) {}
 // IgnoredError implements UploadProgress.
 func (p *NullUploadProgress) IgnoredError(path string, err error) {}
 
-// Checkpoint implements UploadProgress.
-func (p *NullUploadProgress) Checkpoint() {}
-
 var _ UploadProgress = (*NullUploadProgress)(nil)
 
 // UploadCounters represents a snapshot of upload counters.
diff --git a/snapshot/snapshotfs/upload_test.go b/snapshot/snapshotfs/upload_test.go
index 96b0d4b83..c25787a14 100644
--- a/snapshot/snapshotfs/upload_test.go
+++ b/snapshot/snapshotfs/upload_test.go
@@ -13,6 +13,7 @@
 	"github.com/pkg/errors"
 
 	"github.com/kopia/kopia/fs"
+	"github.com/kopia/kopia/internal/clock"
 	"github.com/kopia/kopia/internal/faketime"
 	"github.com/kopia/kopia/internal/mockfs"
 	"github.com/kopia/kopia/internal/testlogging"
@@ -289,6 +290,16 @@ func TestUploadWithCheckpointing(t *testing.T) {
 
 	u := NewUploader(th.repo)
 
+	fakeTicker := make(chan time.Time)
+
+	// inject fake ticker that we can control externally instead of through time passage.
+	u.getTicker = func(d time.Duration) <-chan time.Time {
+		return fakeTicker
+	}
+
+	// create a channel that will be sent to whenever checkpoint completes.
+	u.checkpointFinished = make(chan struct{})
+
 	policyTree := policy.BuildTree(nil, policy.DefaultPolicy)
 
 	si := snapshot.SourceInfo{
@@ -297,18 +308,22 @@ func TestUploadWithCheckpointing(t *testing.T) {
 		Path:     "path",
 	}
 
-	count := 0
+	// inject a hook into mock filesystem to trigger and wait for checkpoints at few places.
+	// the places are not important, what's important that those are 3 separate points in time.
+	dirsToCheckpointAt := []*mockfs.Directory{
+		th.sourceDir.Subdir("d1"),
+		th.sourceDir.Subdir("d2"),
+		th.sourceDir.Subdir("d1").Subdir("d2"),
+	}
 
-	// when reading d1 advanced the time, to trigger checkpoint
-	th.sourceDir.Subdir("d1").OnReaddir(func() {
-		count++
-
-		// when reading this directory advance the time to cancel the snapshot
-		// and trigger a checkpoint
-		if count <= 2 {
-			th.ft.Advance(DefaultCheckpointInterval + 1)
-		}
-	})
+	for _, d := range dirsToCheckpointAt {
+		d.OnReaddir(func() {
+			// trigger checkpoint
+			fakeTicker <- clock.Now()
+			// wait for checkpoint
+			<-u.checkpointFinished
+		})
+	}
 
 	if _, err := u.Upload(ctx, th.sourceDir, policyTree, si); err != nil {
 		t.Errorf("Upload error: %v", err)
@@ -319,7 +334,7 @@ func TestUploadWithCheckpointing(t *testing.T) {
 		t.Fatalf("error listing snapshots: %v", err)
 	}
 
-	if got, want := len(snapshots), 2; got != want {
+	if got, want := len(snapshots), len(dirsToCheckpointAt); got != want {
 		t.Fatalf("unexpected number of snapshots: %v, want %v", got, want)
 	}
 
diff --git a/snapshot/stats.go b/snapshot/stats.go
index aa57143bf..470d18031 100644
--- a/snapshot/stats.go
+++ b/snapshot/stats.go
@@ -6,17 +6,20 @@
 
 // Stats keeps track of snapshot generation statistics.
 type Stats struct {
-	TotalDirectoryCount int   `json:"dirCount"`
-	TotalFileCount      int   `json:"fileCount"`
-	TotalFileSize       int64 `json:"totalSize"`
-
-	ExcludedFileCount     int   `json:"excludedFileCount"`
+	// keep all int64 aligned because they will be atomically updated
+	TotalFileSize         int64 `json:"totalSize"`
 	ExcludedTotalFileSize int64 `json:"excludedTotalSize"`
-	ExcludedDirCount      int   `json:"excludedDirCount"`
 
+	// keep all int32 aligned because they will be atomically updated
+	TotalFileCount int32 `json:"fileCount"`
 	CachedFiles    int32 `json:"cachedFiles"`
 	NonCachedFiles int32 `json:"nonCachedFiles"`
 
+	TotalDirectoryCount int `json:"dirCount"`
+
+	ExcludedFileCount int `json:"excludedFileCount"`
+	ExcludedDirCount  int `json:"excludedDirCount"`
+
 	ReadErrors int `json:"readErrors"`
 }