diff --git a/.changeset/forty-lies-work.md b/.changeset/forty-lies-work.md
new file mode 100644
index 0000000000..21bb8e27fa
--- /dev/null
+++ b/.changeset/forty-lies-work.md
@@ -0,0 +1,33 @@
+---
+"@pnpm/resolve-dependencies": patch
+"supi": patch
+---
+
+The lockfile should be correctly updated when a direct dependency that has peer dependencies has a new version specifier in `package.json`.
+
+For instance, `jest@26` has `cascade@2` in its peer dependencies. So `pnpm install` will scope Jest to some version of cascade. This is how it will look like in `pnpm-lock.yaml`:
+
+```yaml
+dependencies:
+  canvas: 2.6.0
+  jest: 26.4.0_canvas@2.6.0
+```
+
+If the version specifier of Jest gets changed in the `package.json` to `26.5.0`, the next time `pnpm install` is executed, the lockfile should be changed to this:
+
+```yaml
+dependencies:
+  canvas: 2.6.0
+  jest: 26.5.0_canvas@2.6.0
+```
+
+Prior to this fix, after the update, Jest was not scoped with canvas, so the lockfile was incorrectly updated to the following:
+
+```yaml
+dependencies:
+  canvas: 2.6.0
+  jest: 26.5.0
+```
+
+Related issue: [#2919](https://github.com/pnpm/pnpm/issues/2919).
+Related PR: [#2920](https://github.com/pnpm/pnpm/pull/2920).
diff --git a/packages/plugin-commands-installation/test/index.ts b/packages/plugin-commands-installation/test/index.ts
index d378ee16ea..b5d7460408 100644
--- a/packages/plugin-commands-installation/test/index.ts
+++ b/packages/plugin-commands-installation/test/index.ts
@@ -3,6 +3,7 @@ import './add'
 import './addRecursive'
 import './linkRecursive'
 import './miscRecursive'
+import './peerDependencies'
 import './prune'
 import './remove/completion'
 import './remove/remove'
diff --git a/packages/plugin-commands-installation/test/peerDependencies.ts b/packages/plugin-commands-installation/test/peerDependencies.ts
new file mode 100644
index 0000000000..98c3da7a0b
--- /dev/null
+++ b/packages/plugin-commands-installation/test/peerDependencies.ts
@@ -0,0 +1,68 @@
+import { add, install } from '@pnpm/plugin-commands-installation'
+import prepare from '@pnpm/prepare'
+import { REGISTRY_MOCK_PORT } from '@pnpm/registry-mock'
+import test = require('tape')
+import tempy = require('tempy')
+
+const REGISTRY_URL = `http://localhost:${REGISTRY_MOCK_PORT}`
+
+const DEFAULT_OPTIONS = {
+  argv: {
+    original: [],
+  },
+  bail: false,
+  cliOptions: {},
+  include: {
+    dependencies: true,
+    devDependencies: true,
+    optionalDependencies: true,
+  },
+  lock: true,
+  pnpmfile: 'pnpmfile.js',
+  rawConfig: { registry: REGISTRY_URL },
+  rawLocalConfig: { registry: REGISTRY_URL },
+  registries: {
+    default: REGISTRY_URL,
+  },
+  sort: true,
+  storeDir: tempy.directory(),
+  workspaceConcurrency: 1,
+}
+
+test('root dependency that has a peer is correctly updated after its version changes', async (t) => {
+  const project = prepare(t, {})
+
+  await add.handler({
+    ...DEFAULT_OPTIONS,
+    dir: process.cwd(),
+    linkWorkspacePackages: true,
+  }, ['ajv@4.10.4', 'ajv-keywords@1.5.0'])
+
+  {
+    const lockfile = await project.readLockfile()
+    t.equal(lockfile.dependencies['ajv-keywords'], '1.5.0_ajv@4.10.4')
+  }
+
+  await project.writePackageJson({
+    dependencies: {
+      ajv: '4.10.4',
+      'ajv-keywords': '1.5.1',
+    },
+  })
+
+  await install.handler({
+    ...DEFAULT_OPTIONS,
+    dir: process.cwd(),
+    linkWorkspacePackages: true,
+    rawLocalConfig: {
+      'frozen-lockfile': false,
+    },
+  })
+
+  {
+    const lockfile = await project.readLockfile()
+    t.equal(lockfile.dependencies['ajv-keywords'], '1.5.1_ajv@4.10.4')
+  }
+
+  t.end()
+})
diff --git a/packages/resolve-dependencies/src/resolveDependencies.ts b/packages/resolve-dependencies/src/resolveDependencies.ts
index a60f500462..10c4592656 100644
--- a/packages/resolve-dependencies/src/resolveDependencies.ts
+++ b/packages/resolve-dependencies/src/resolveDependencies.ts
@@ -358,7 +358,7 @@ function getDepsToResolve (
   // The only reason we resolve children in case the package depends on peers
   // is to get information about the existing dependencies, so that they can
   // be merged with the resolved peers.
-  const proceedAll = options.proceed
+  let proceedAll = options.proceed
   const allPeers = new Set<string>()
   for (const wantedDependency of wantedDependencies) {
     let reference = wantedDependency.alias && resolvedDependencies[wantedDependency.alias]
@@ -394,6 +394,15 @@ function getDepsToResolve (
         allPeers.add(peerName)
       })
     }
+    if (!infoFromLockfile && !proceedAll) {
+      // In this case we don't know if the package depends on peer dependencies, so we proceed all.
+      proceedAll = true
+      for (const extendedWantedDep of extendedWantedDeps) {
+        if (!extendedWantedDep.proceed) {
+          extendedWantedDep.proceed = true
+        }
+      }
+    }
     extendedWantedDeps.push({
       infoFromLockfile,
       proceed,
diff --git a/packages/supi/src/install/index.ts b/packages/supi/src/install/index.ts
index f72a25b007..9d9351d016 100644
--- a/packages/supi/src/install/index.ts
+++ b/packages/supi/src/install/index.ts
@@ -850,7 +850,7 @@ async function toResolveImporter (
   project: ImporterToUpdate
 ) {
   const allDeps = getWantedDependencies(project.manifest)
-  const { linkedAliases, nonLinkedDependencies } = await partitionLinkedPackages(allDeps, {
+  const { nonLinkedDependencies } = await partitionLinkedPackages(allDeps, {
     lockfileOnly: opts.lockfileOnly,
     modulesDir: project.modulesDir,
     projectDir: project.rootDir,
@@ -890,8 +890,7 @@ async function toResolveImporter (
     ...project,
     hasRemovedDependencies: Boolean(project.removePackages?.length),
     preferredVersions: opts.preferredVersions ?? (project.manifest && getPreferredVersionsFromPackage(project.manifest)) ?? {},
-    wantedDependencies: wantedDependencies
-      .filter(({ alias, updateDepth }) => updateDepth >= 0 || !linkedAliases.has(alias)),
+    wantedDependencies,
   }
 }