diff --git a/app/flatpak-builtins-add-remote.c b/app/flatpak-builtins-add-remote.c
index 7f692f73..92193441 100644
--- a/app/flatpak-builtins-add-remote.c
+++ b/app/flatpak-builtins-add-remote.c
@@ -455,7 +455,7 @@ flatpak_builtin_modify_remote (int argc, char **argv, GCancellable *cancellable,
 {
   g_autoptr(GOptionContext) context = NULL;
   g_autoptr(GPtrArray) dirs = NULL;
-  FlatpakDir *dir;
+  g_autoptr(FlatpakDir) preferred_dir = NULL;
   g_autoptr(GKeyFile) config = NULL;
   g_autoptr(GBytes) gpg_data = NULL;
   const char *remote_name;
@@ -467,18 +467,18 @@ flatpak_builtin_modify_remote (int argc, char **argv, GCancellable *cancellable,
   g_option_context_add_main_entries (context, common_options, NULL);
 
   if (!flatpak_option_context_parse (context, modify_options, &argc, &argv,
-                                     FLATPAK_BUILTIN_FLAG_ONE_DIR,
-                                     &dirs, cancellable, error))
+                                     FLATPAK_BUILTIN_FLAG_STANDARD_DIRS, &dirs, cancellable, error))
     return FALSE;
 
-  dir = g_ptr_array_index (dirs, 0);
-
   if (argc < 2)
     return usage_error (context, _("Remote NAME must be specified"), error);
 
   remote_name = argv[1];
 
-  if (!ostree_repo_remote_get_url (flatpak_dir_get_repo (dir), remote_name, NULL, NULL))
+  if (!flatpak_resolve_duplicate_remotes (dirs, remote_name, &preferred_dir, cancellable, error))
+    return FALSE;
+
+  if (!ostree_repo_remote_get_url (flatpak_dir_get_repo (preferred_dir), remote_name, NULL, NULL))
     return flatpak_fail (error, _("No remote %s"), remote_name);
 
   if (opt_update_metadata)
@@ -486,18 +486,18 @@ flatpak_builtin_modify_remote (int argc, char **argv, GCancellable *cancellable,
       g_autoptr(GError) local_error = NULL;
 
       g_print (_("Updating extra metadata from remote summary for %s\n"), remote_name);
-      if (!flatpak_dir_update_remote_configuration (dir, remote_name, cancellable, &local_error))
+      if (!flatpak_dir_update_remote_configuration (preferred_dir, remote_name, cancellable, &local_error))
         {
           g_printerr (_("Error updating extra metadata for '%s': %s\n"), remote_name, local_error->message);
           return flatpak_fail (error, _("Could not update extra metadata for %s"), remote_name);
         }
 
       /* Reload changed configuration */
-      if (!flatpak_dir_recreate_repo (dir, cancellable, error))
+      if (!flatpak_dir_recreate_repo (preferred_dir, cancellable, error))
         return FALSE;
     }
 
-  config = get_config_from_opts (dir, remote_name, &changed);
+  config = get_config_from_opts (preferred_dir, remote_name, &changed);
 
   if (opt_gpg_import != NULL)
     {
@@ -510,7 +510,7 @@ flatpak_builtin_modify_remote (int argc, char **argv, GCancellable *cancellable,
   if (!changed)
     return TRUE;
 
-  return flatpak_dir_modify_remote (dir, remote_name, config, gpg_data, cancellable, error);
+  return flatpak_dir_modify_remote (preferred_dir, remote_name, config, gpg_data, cancellable, error);
 }
 
 gboolean
@@ -518,17 +518,14 @@ flatpak_complete_modify_remote (FlatpakCompletion *completion)
 {
   g_autoptr(GOptionContext) context = NULL;
   g_autoptr(GPtrArray) dirs = NULL;
-  FlatpakDir *dir;
   int i;
 
   context = g_option_context_new ("");
   g_option_context_add_main_entries (context, common_options, NULL);
   if (!flatpak_option_context_parse (context, modify_options, &completion->argc, &completion->argv,
-                                     FLATPAK_BUILTIN_FLAG_ONE_DIR, &dirs, NULL, NULL))
+                                     FLATPAK_BUILTIN_FLAG_STANDARD_DIRS, &dirs, NULL, NULL))
     return FALSE;
 
-  dir = g_ptr_array_index (dirs, 0);
-
   switch (completion->argc)
     {
     case 0:
@@ -538,13 +535,16 @@ flatpak_complete_modify_remote (FlatpakCompletion *completion)
       flatpak_complete_options (completion, modify_options);
       flatpak_complete_options (completion, user_entries);
 
-      {
-        g_auto(GStrv) remotes = flatpak_dir_list_remotes (dir, NULL, NULL);
-        if (remotes == NULL)
-          return FALSE;
-        for (i = 0; remotes[i] != NULL; i++)
-          flatpak_complete_word (completion, "%s ", remotes[i]);
-      }
+      for (i = 0; i < dirs->len; i++)
+        {
+          FlatpakDir *dir = g_ptr_array_index (dirs, i);
+          int j;
+          g_auto(GStrv) remotes = flatpak_dir_list_remotes (dir, NULL, NULL);
+          if (remotes == NULL)
+            return FALSE;
+          for (j = 0; remotes[j] != NULL; j++)
+            flatpak_complete_word (completion, "%s ", remotes[j]);
+        }
 
       break;
     }
diff --git a/app/flatpak-builtins-delete-remote.c b/app/flatpak-builtins-delete-remote.c
index c84ea27e..f23470ff 100644
--- a/app/flatpak-builtins-delete-remote.c
+++ b/app/flatpak-builtins-delete-remote.c
@@ -30,6 +30,7 @@
 #include "libglnx/libglnx.h"
 
 #include "flatpak-builtins.h"
+#include "flatpak-builtins-utils.h"
 
 static gboolean opt_force;
 
@@ -44,7 +45,7 @@ flatpak_builtin_delete_remote (int argc, char **argv, GCancellable *cancellable,
 {
   g_autoptr(GOptionContext) context = NULL;
   g_autoptr(GPtrArray) dirs = NULL;
-  FlatpakDir *dir;
+  g_autoptr(FlatpakDir) preferred_dir = NULL;
   const char *remote_name;
 
   context = g_option_context_new (_("NAME - Delete a remote repository"));
@@ -53,12 +54,9 @@ flatpak_builtin_delete_remote (int argc, char **argv, GCancellable *cancellable,
   g_option_context_add_main_entries (context, delete_options, NULL);
 
   if (!flatpak_option_context_parse (context, NULL, &argc, &argv,
-                                     FLATPAK_BUILTIN_FLAG_ONE_DIR,
-                                     &dirs, cancellable, error))
+                                     FLATPAK_BUILTIN_FLAG_STANDARD_DIRS, &dirs, cancellable, error))
     return FALSE;
 
-  dir = g_ptr_array_index (dirs, 0);
-
   if (argc < 2)
     return usage_error (context, _("NAME must be specified"), error);
 
@@ -67,7 +65,10 @@ flatpak_builtin_delete_remote (int argc, char **argv, GCancellable *cancellable,
   if (argc > 2)
     return usage_error (context, _("Too many arguments"), error);
 
-  if (!flatpak_dir_remove_remote (dir, opt_force, remote_name,
+  if (!flatpak_resolve_duplicate_remotes (dirs, remote_name, &preferred_dir, cancellable, error))
+    return FALSE;
+
+  if (!flatpak_dir_remove_remote (preferred_dir, opt_force, remote_name,
                                   cancellable, error))
     return FALSE;
 
@@ -79,16 +80,13 @@ flatpak_complete_delete_remote (FlatpakCompletion *completion)
 {
   g_autoptr(GOptionContext) context = NULL;
   g_autoptr(GPtrArray) dirs = NULL;
-  FlatpakDir *dir;
   int i;
 
   context = g_option_context_new ("");
   if (!flatpak_option_context_parse (context, delete_options, &completion->argc, &completion->argv,
-                                     FLATPAK_BUILTIN_FLAG_ONE_DIR, &dirs, NULL, NULL))
+                                     FLATPAK_BUILTIN_FLAG_STANDARD_DIRS, &dirs, NULL, NULL))
     return FALSE;
 
-  dir = g_ptr_array_index (dirs, 0);
-
   switch (completion->argc)
     {
     case 0:
@@ -97,13 +95,16 @@ flatpak_complete_delete_remote (FlatpakCompletion *completion)
       flatpak_complete_options (completion, delete_options);
       flatpak_complete_options (completion, user_entries);
 
-      {
-        g_auto(GStrv) remotes = flatpak_dir_list_remotes (dir, NULL, NULL);
-        if (remotes == NULL)
-          return FALSE;
-        for (i = 0; remotes[i] != NULL; i++)
-          flatpak_complete_word (completion, "%s ", remotes[i]);
-      }
+      for (i = 0; i < dirs->len; i++)
+        {
+          FlatpakDir *dir = g_ptr_array_index (dirs, i);
+          int j;
+          g_auto(GStrv) remotes = flatpak_dir_list_remotes (dir, NULL, NULL);
+          if (remotes == NULL)
+            return FALSE;
+          for (j = 0; remotes[j] != NULL; j++)
+            flatpak_complete_word (completion, "%s ", remotes[j]);
+        }
 
       break;
     }
diff --git a/app/flatpak-builtins-info-remote.c b/app/flatpak-builtins-info-remote.c
index 56a147ba..93168623 100644
--- a/app/flatpak-builtins-info-remote.c
+++ b/app/flatpak-builtins-info-remote.c
@@ -30,6 +30,7 @@
 #include "libglnx/libglnx.h"
 
 #include "flatpak-builtins.h"
+#include "flatpak-builtins-utils.h"
 #include "flatpak-utils.h"
 #include "flatpak-table-printer.h"
 
@@ -87,7 +88,7 @@ flatpak_builtin_info_remote (int argc, char **argv, GCancellable *cancellable, G
 {
   g_autoptr(GOptionContext) context = NULL;
   g_autoptr(GPtrArray) dirs = NULL;
-  FlatpakDir *dir;
+  g_autoptr(FlatpakDir) preferred_dir = NULL;
   g_autoptr(GVariant) commit_v = NULL;
   g_autoptr(GVariant) commit_metadata = NULL;
   const char *remote;
@@ -121,12 +122,9 @@ flatpak_builtin_info_remote (int argc, char **argv, GCancellable *cancellable, G
   g_option_context_set_translation_domain (context, GETTEXT_PACKAGE);
 
   if (!flatpak_option_context_parse (context, options, &argc, &argv,
-                                     FLATPAK_BUILTIN_FLAG_ONE_DIR,
-                                     &dirs, cancellable, error))
+                                     FLATPAK_BUILTIN_FLAG_STANDARD_DIRS, &dirs, cancellable, error))
     return FALSE;
 
-  dir = g_ptr_array_index (dirs, 0);
-
   if (!opt_app && !opt_runtime)
     opt_app = opt_runtime = TRUE;
 
@@ -136,19 +134,22 @@ flatpak_builtin_info_remote (int argc, char **argv, GCancellable *cancellable, G
   remote = argv[1];
   pref = argv[2];
 
-  default_branch = flatpak_dir_get_remote_default_branch (dir, remote);
+  if (!flatpak_resolve_duplicate_remotes (dirs, remote, &preferred_dir, cancellable, error))
+    return FALSE;
+
+  default_branch = flatpak_dir_get_remote_default_branch (preferred_dir, remote);
   kinds = flatpak_kinds_from_bools (opt_app, opt_runtime);
 
   if (!flatpak_split_partial_ref_arg (pref, kinds, opt_arch, NULL,
                                       &matched_kinds, &id, &arch, &branch, error))
     return FALSE;
 
-  ref = flatpak_dir_find_remote_ref (dir, remote, id, branch, default_branch, arch,
+  ref = flatpak_dir_find_remote_ref (preferred_dir, remote, id, branch, default_branch, arch,
                                      matched_kinds, &kind, cancellable, error);
   if (ref == NULL)
     return FALSE;
 
-  commit_v = flatpak_dir_fetch_remote_commit (dir, remote, ref, opt_commit, &commit, cancellable, error);
+  commit_v = flatpak_dir_fetch_remote_commit (preferred_dir, remote, ref, opt_commit, &commit, cancellable, error);
   if (commit_v == NULL)
     return FALSE;
 
@@ -220,7 +221,7 @@ flatpak_builtin_info_remote (int argc, char **argv, GCancellable *cancellable, G
               g_autofree char *p_formatted_timestamp = NULL;
               g_autoptr(GVariant) p_commit_v = NULL;
 
-              p_commit_v = flatpak_dir_fetch_remote_commit (dir, remote, ref, p, NULL, cancellable, NULL);
+              p_commit_v = flatpak_dir_fetch_remote_commit (preferred_dir, remote, ref, p, NULL, cancellable, NULL);
               if (p_commit_v == NULL)
                 break;
 
@@ -282,7 +283,7 @@ flatpak_builtin_info_remote (int argc, char **argv, GCancellable *cancellable, G
           c_v = NULL;
 
           if (c && opt_log)
-            c_v = flatpak_dir_fetch_remote_commit (dir, remote, ref, c, NULL, cancellable, NULL);
+            c_v = flatpak_dir_fetch_remote_commit (preferred_dir, remote, ref, c, NULL, cancellable, NULL);
         }
       while (c_v != NULL);
     }
@@ -295,18 +296,15 @@ flatpak_complete_info_remote (FlatpakCompletion *completion)
 {
   g_autoptr(GOptionContext) context = NULL;
   g_autoptr(GPtrArray) dirs = NULL;
-  FlatpakDir *dir;
   FlatpakKinds kinds;
   int i;
 
   context = g_option_context_new ("");
 
   if (!flatpak_option_context_parse (context, options, &completion->argc, &completion->argv,
-                                     FLATPAK_BUILTIN_FLAG_ONE_DIR, &dirs, NULL, NULL))
+                                     FLATPAK_BUILTIN_FLAG_STANDARD_DIRS, &dirs, NULL, NULL))
     return FALSE;
 
-  dir = g_ptr_array_index (dirs, 0);
-
   kinds = flatpak_kinds_from_bools (opt_app, opt_runtime);
 
   switch (completion->argc)
@@ -317,18 +315,26 @@ flatpak_complete_info_remote (FlatpakCompletion *completion)
       flatpak_complete_options (completion, options);
       flatpak_complete_options (completion, user_entries);
 
-      {
-        g_auto(GStrv) remotes = flatpak_dir_list_remotes (dir, NULL, NULL);
-        if (remotes == NULL)
-          return FALSE;
-        for (i = 0; remotes[i] != NULL; i++)
-          flatpak_complete_word (completion, "%s ", remotes[i]);
-      }
+      for (i = 0; i < dirs->len; i++)
+        {
+          FlatpakDir *dir = g_ptr_array_index (dirs, i);
+          int j;
+          g_auto(GStrv) remotes = flatpak_dir_list_remotes (dir, NULL, NULL);
+          if (remotes == NULL)
+            return FALSE;
+          for (j = 0; remotes[j] != NULL; j++)
+            flatpak_complete_word (completion, "%s ", remotes[j]);
+        }
 
       break;
 
     default: /* REF */
-      flatpak_complete_partial_ref (completion, kinds, opt_arch, dir, completion->argv[1]);
+      for (i = 0; i < dirs->len; i++)
+        {
+          FlatpakDir *dir = g_ptr_array_index (dirs, i);
+          flatpak_complete_partial_ref (completion, kinds, opt_arch, dir, completion->argv[1]);
+        }
+
       break;
     }
 
diff --git a/app/flatpak-builtins-ls-remote.c b/app/flatpak-builtins-ls-remote.c
index f59fc43e..c1614a50 100644
--- a/app/flatpak-builtins-ls-remote.c
+++ b/app/flatpak-builtins-ls-remote.c
@@ -30,6 +30,7 @@
 #include "libglnx/libglnx.h"
 
 #include "flatpak-builtins.h"
+#include "flatpak-builtins-utils.h"
 #include "flatpak-utils.h"
 #include "flatpak-table-printer.h"
 
@@ -50,12 +51,33 @@ static GOptionEntry options[] = {
   { NULL }
 };
 
+typedef struct RemoteDirPair {
+  gchar *remote_name;
+  FlatpakDir *dir;
+} RemoteDirPair;
+
+static void
+remote_dir_pair_free (RemoteDirPair *pair)
+{
+  g_free (pair->remote_name);
+  g_object_unref (pair->dir);
+  g_free (pair);
+}
+
+static RemoteDirPair *
+remote_dir_pair_new (const char *remote_name, FlatpakDir *dir)
+{
+  RemoteDirPair *pair = g_new (RemoteDirPair, 1);
+  pair->remote_name = g_strdup (remote_name);
+  pair->dir = g_object_ref (dir);
+  return pair;
+}
+
 gboolean
 flatpak_builtin_ls_remote (int argc, char **argv, GCancellable *cancellable, GError **error)
 {
   g_autoptr(GOptionContext) context = NULL;
   g_autoptr(GPtrArray) dirs = NULL;
-  FlatpakDir *dir;
   GHashTableIter refs_iter;
   GHashTableIter iter;
   gpointer refs_key;
@@ -67,54 +89,72 @@ flatpak_builtin_ls_remote (int argc, char **argv, GCancellable *cancellable, GEr
   int i;
   const char **arches = flatpak_get_arches ();
   const char *opt_arches[] = {NULL, NULL};
-  g_auto(GStrv) remotes = NULL;
   gboolean has_remote;
   g_autoptr(GHashTable) pref_hash = g_hash_table_new_full (g_str_hash, g_str_equal, g_free, NULL);
-  g_autoptr(GHashTable) refs_hash = g_hash_table_new_full(g_direct_hash, g_direct_equal, (GDestroyNotify)g_hash_table_unref, g_free);
+  g_autoptr(GHashTable) refs_hash = g_hash_table_new_full(g_direct_hash, g_direct_equal, (GDestroyNotify)g_hash_table_unref, (GDestroyNotify)remote_dir_pair_free);
 
   context = g_option_context_new (_(" [REMOTE] - Show available runtimes and applications"));
   g_option_context_set_translation_domain (context, GETTEXT_PACKAGE);
 
   if (!flatpak_option_context_parse (context, options, &argc, &argv,
-                                     FLATPAK_BUILTIN_FLAG_ONE_DIR,
-                                     &dirs, cancellable, error))
+                                     FLATPAK_BUILTIN_FLAG_STANDARD_DIRS, &dirs, cancellable, error))
     return FALSE;
 
-  dir = g_ptr_array_index (dirs, 0);
-
   if (!opt_app && !opt_runtime)
     opt_app = opt_runtime = TRUE;
 
   if (argc > 2)
     return usage_error (context, _("Too many arguments"), error);
 
-  if (argc < 2)
-    {
-      has_remote = FALSE;
-      remotes = flatpak_dir_list_remotes (dir, cancellable, error);
-      if (remotes == NULL)
-        return FALSE;
-    }
-  else
-    {
-      has_remote = TRUE;
-      remotes = g_new (char *, 2);
-      remotes[0] = g_strdup(argv[1]);
-      remotes[1] = NULL;
-    }
+  has_remote = (argc == 2);
 
-  for (i = 0; remotes[i] != NULL; i++)
+  if (has_remote)
     {
+      g_autoptr(FlatpakDir) preferred_dir = NULL;
       g_autoptr(GHashTable) refs = NULL;
-      const char *remote_name = remotes[i];
+      RemoteDirPair *remote_dir_pair = NULL;
 
-      if (!flatpak_dir_list_remote_refs (dir,
-                                         remote_name,
+      if (!flatpak_resolve_duplicate_remotes (dirs, argv[1], &preferred_dir, cancellable, error))
+        return FALSE;
+
+      if (!flatpak_dir_list_remote_refs (preferred_dir,
+                                         argv[1],
                                          &refs,
                                          cancellable, error))
         return FALSE;
 
-      g_hash_table_insert (refs_hash, g_steal_pointer (&refs), g_strdup (remote_name));
+      remote_dir_pair = remote_dir_pair_new (argv[1], preferred_dir);
+      g_hash_table_insert (refs_hash, g_steal_pointer (&refs), remote_dir_pair);
+    }
+  else
+    {
+      int i;
+      for (i = 0; i < dirs->len; i++)
+        {
+          FlatpakDir *dir = g_ptr_array_index (dirs, i);
+          g_auto(GStrv) remotes = NULL;
+          int j;
+
+          remotes = flatpak_dir_list_remotes (dir, cancellable, error);
+          if (remotes == NULL)
+            return FALSE;
+
+          for (j = 0; remotes[j] != NULL; j++)
+            {
+              g_autoptr(GHashTable) refs = NULL;
+              RemoteDirPair *remote_dir_pair = NULL;
+              const char *remote_name = remotes[j];
+
+              if (!flatpak_dir_list_remote_refs (dir,
+                                                 remote_name,
+                                                 &refs,
+                                                 cancellable, error))
+                return FALSE;
+
+              remote_dir_pair = remote_dir_pair_new (remote_name, dir);
+              g_hash_table_insert (refs_hash, g_steal_pointer (&refs), remote_dir_pair);
+            }
+        }
     }
 
   if (opt_arch != NULL)
@@ -142,7 +182,9 @@ flatpak_builtin_ls_remote (int argc, char **argv, GCancellable *cancellable, GEr
   while (g_hash_table_iter_next (&refs_iter, &refs_key, &refs_value))
     {
       GHashTable *refs = refs_key;
-      char *remote = refs_value;
+      RemoteDirPair *remote_dir_pair = refs_value;
+      const char *remote = remote_dir_pair->remote_name;
+      FlatpakDir *dir = remote_dir_pair->dir;
       g_autoptr(GHashTable) names = g_hash_table_new_full (g_str_hash, g_str_equal, g_free, g_free);
 
       g_hash_table_iter_init (&iter, refs);
@@ -285,17 +327,14 @@ flatpak_complete_ls_remote (FlatpakCompletion *completion)
 {
   g_autoptr(GOptionContext) context = NULL;
   g_autoptr(GPtrArray) dirs = NULL;
-  FlatpakDir *dir;
   int i;
 
   context = g_option_context_new ("");
 
   if (!flatpak_option_context_parse (context, options, &completion->argc, &completion->argv,
-                                     FLATPAK_BUILTIN_FLAG_ONE_DIR, &dirs, NULL, NULL))
+                                     FLATPAK_BUILTIN_FLAG_STANDARD_DIRS, &dirs, NULL, NULL))
     return FALSE;
 
-  dir = g_ptr_array_index (dirs, 0);
-
   switch (completion->argc)
     {
     case 0:
@@ -304,13 +343,16 @@ flatpak_complete_ls_remote (FlatpakCompletion *completion)
       flatpak_complete_options (completion, options);
       flatpak_complete_options (completion, user_entries);
 
-      {
-        g_auto(GStrv) remotes = flatpak_dir_list_remotes (dir, NULL, NULL);
-        if (remotes == NULL)
-          return FALSE;
-        for (i = 0; remotes[i] != NULL; i++)
-          flatpak_complete_word (completion, "%s ", remotes[i]);
-      }
+      for (i = 0; i < dirs->len; i++)
+        {
+          FlatpakDir *dir = g_ptr_array_index (dirs, i);
+          int j;
+          g_auto(GStrv) remotes = flatpak_dir_list_remotes (dir, NULL, NULL);
+          if (remotes == NULL)
+            return FALSE;
+          for (j = 0; remotes[j] != NULL; j++)
+            flatpak_complete_word (completion, "%s ", remotes[j]);
+        }
 
       break;
     }
diff --git a/app/flatpak-builtins-utils.c b/app/flatpak-builtins-utils.c
index 56eeb3ea..0c874912 100644
--- a/app/flatpak-builtins-utils.c
+++ b/app/flatpak-builtins-utils.c
@@ -326,3 +326,65 @@ flatpak_load_gpg_keys (char **gpg_import,
 
   return g_memory_output_stream_steal_as_bytes (G_MEMORY_OUTPUT_STREAM (output_stream));
 }
+
+gboolean
+flatpak_resolve_duplicate_remotes (GPtrArray    *dirs,
+                                   const char   *remote_name,
+                                   FlatpakDir  **out_dir,
+                                   GCancellable *cancellable,
+                                   GError      **error)
+{
+  g_autoptr(GPtrArray) dirs_with_remote = NULL;
+  int chosen = 0;
+  int i;
+
+  dirs_with_remote = g_ptr_array_new ();
+  for (i = 0; i < dirs->len; i++)
+    {
+      FlatpakDir *dir = g_ptr_array_index (dirs, i);
+      g_auto(GStrv) remotes = NULL;
+      int j = 0;
+
+      remotes = flatpak_dir_list_remotes (dir, cancellable, error);
+      if (remotes == NULL)
+        return FALSE;
+
+      for (j = 0; remotes[j] != NULL; j++)
+        {
+          const char *this_remote = remotes[j];
+
+          if (g_strcmp0 (remote_name, this_remote) == 0)
+            g_ptr_array_add (dirs_with_remote, dir);
+        }
+    }
+
+  if (dirs_with_remote->len == 1)
+    chosen = 1;
+  else if (dirs_with_remote->len > 1)
+    {
+      g_print (_("Remote ‘%s’ found in multiple installations:\n"), remote_name);
+      for (i = 0; i < dirs_with_remote->len; i++)
+        {
+          FlatpakDir *dir = g_ptr_array_index (dirs_with_remote, i);
+          g_autofree char *dir_name = flatpak_dir_get_name (dir);
+          g_print("%d) %s\n", i + 1, dir_name);
+        }
+      chosen = flatpak_number_prompt (1, dirs_with_remote->len, _("Which do you want to use (0 to abort)?"));
+      if (chosen == 0)
+        return flatpak_fail (error, _("No remote chosen to resolve ‘%s’ which exists in multiple installations"), remote_name);
+    }
+
+  if (out_dir)
+    {
+      if (dirs_with_remote->len == 0)
+        {
+          g_set_error (error, G_IO_ERROR, G_IO_ERROR_NOT_FOUND,
+                       "Remote \"%s\" not found", remote_name);
+          return FALSE;
+        }
+      else
+        *out_dir = g_object_ref (g_ptr_array_index (dirs_with_remote, chosen - 1));
+    }
+
+  return TRUE;
+}
diff --git a/app/flatpak-builtins-utils.h b/app/flatpak-builtins-utils.h
index 6d66c931..1ce4aaf7 100644
--- a/app/flatpak-builtins-utils.h
+++ b/app/flatpak-builtins-utils.h
@@ -46,4 +46,10 @@ FlatpakDir * flatpak_find_installed_pref (const char *pref,
                                           GCancellable *cancellable,
                                           GError **error);
 
+gboolean flatpak_resolve_duplicate_remotes (GPtrArray    *dirs,
+                                            const char   *remote_name,
+                                            FlatpakDir  **out_dir,
+                                            GCancellable *cancellable,
+                                            GError      **error);
+
 #endif /* __FLATPAK_BUILTINS_UTILS_H__ */
diff --git a/doc/flatpak-remote-delete.xml b/doc/flatpak-remote-delete.xml
index 6c8ec652..5c2d2540 100644
--- a/doc/flatpak-remote-delete.xml
+++ b/doc/flatpak-remote-delete.xml
@@ -44,8 +44,10 @@
             <arg choice="plain">NAME</arg> is the name of an existing remote.
         </para>
         <para>
-            Unless overridden with the --user or --installation options, this command
-            changes the default system-wide installation.
+            Unless overridden with the --system, --user, or --installation options,
+            this command uses either the default system-wide installation or the
+            per-user one, depending on which has the specified
+            <arg choice="plain">REMOTE</arg>.
         </para>
 
     </refsect1>
diff --git a/doc/flatpak-remote-info.xml b/doc/flatpak-remote-info.xml
index 1f482d81..ffd9bb56 100644
--- a/doc/flatpak-remote-info.xml
+++ b/doc/flatpak-remote-info.xml
@@ -52,8 +52,10 @@
             in a machine-readable format.
         </para>
         <para>
-            Unless overridden with the --user or --installation options, this command
-            uses the default system-wide configuration.
+            Unless overridden with the --system, --user, or --installation options,
+            this command uses either the default system-wide installation or the
+            per-user one, depending on which has the specified
+            <arg choice="plain">REMOTE</arg>.
         </para>
 
     </refsect1>
diff --git a/doc/flatpak-remote-ls.xml b/doc/flatpak-remote-ls.xml
index 7e4ce778..33bcc294 100644
--- a/doc/flatpak-remote-ls.xml
+++ b/doc/flatpak-remote-ls.xml
@@ -46,8 +46,10 @@
             remote repositories with <citerefentry><refentrytitle>flatpak-remotes</refentrytitle><manvolnum>1</manvolnum></citerefentry>.
         </para>
         <para>
-            Unless overridden with the --user or --installation options, this command
-            uses the default system-wide configuration.
+            Unless overridden with the --system, --user, or --installation options,
+            this command uses either the default system-wide installation or the
+            per-user one, depending on which has the specified
+            <arg choice="plain">REMOTE</arg>.
         </para>
 
     </refsect1>
diff --git a/doc/flatpak-remote-modify.xml b/doc/flatpak-remote-modify.xml
index 3f5b58bc..9e961435 100644
--- a/doc/flatpak-remote-modify.xml
+++ b/doc/flatpak-remote-modify.xml
@@ -44,8 +44,10 @@
             <arg choice="plain">NAME</arg> is the name for the remote.
         </para>
         <para>
-            Unless overridden with the --user or --installation options, this command
-            changes the default system-wide installation.
+            Unless overridden with the --system, --user, or --installation options,
+            this command uses either the default system-wide installation or the
+            per-user one, depending on which has the specified
+            <arg choice="plain">REMOTE</arg>.
         </para>
 
     </refsect1>
diff --git a/tests/test-repo.sh b/tests/test-repo.sh
index 76371955..f588ce5b 100755
--- a/tests/test-repo.sh
+++ b/tests/test-repo.sh
@@ -28,7 +28,7 @@ if [ x${USE_COLLECTIONS_IN_CLIENT-} == xyes ] || [ x${USE_COLLECTIONS_IN_SERVER-
     skip_without_p2p
 fi
 
-echo "1..6"
+echo "1..10"
 
 #Regular repo
 setup_repo
@@ -131,4 +131,158 @@ update_repo test-gpg3 org.test.Collection.test
 ${FLATPAK} ${U} install test-repo org.test.Hello
 assert_file_has_content $FL_DIR/app/org.test.Hello/$ARCH/master/active/files/bin/hello.sh UPDATED
 
+${FLATPAK} ${U} uninstall org.test.Platform org.test.Hello
+
 echo "ok redirect url and gpg key"
+
+# Test that remote-ls works in all of the following cases:
+# * system remote, and --system is used
+# * system remote, and --system is omitted
+# * user remote, and --user is used
+# * user remote, and --user is omitted
+# and fails in the following cases:
+# * system remote, and --user is used
+# * user remote, and --system is used
+if [ x${USE_SYSTEMDIR-} == xyes ]; then
+    ${FLATPAK} --system remote-ls test-repo > repo-list
+    assert_file_has_content repo-list "org.test.Hello"
+
+    ${FLATPAK} remote-ls test-repo > repo-list
+    assert_file_has_content repo-list "org.test.Hello"
+
+    if ${FLATPAK} --user remote-ls test-repo 2> remote-ls-error-log; then
+        assert_not_reached "flatpak --user remote-ls should not work for system remotes"
+    fi
+    assert_file_has_content remote-ls-error-log "Remote \"test-repo\" not found"
+else
+    ${FLATPAK} --user remote-ls test-repo > repo-list
+    assert_file_has_content repo-list "org.test.Hello"
+
+    ${FLATPAK} remote-ls test-repo > repo-list
+    assert_file_has_content repo-list "org.test.Hello"
+
+    if ${FLATPAK} --system remote-ls test-repo 2> remote-ls-error-log; then
+        assert_not_reached "flatpak --system remote-ls should not work for user remotes"
+    fi
+    assert_file_has_content remote-ls-error-log "Remote \"test-repo\" not found"
+fi
+
+echo "ok remote-ls"
+
+# Test that remote-modify works in all of the following cases:
+# * system remote, and --system is used
+# * system remote, and --system is omitted
+# * user remote, and --user is used
+# * user remote, and --user is omitted
+# and fails in the following cases:
+# * system remote, and --user is used
+# * user remote, and --system is used
+if [ x${USE_SYSTEMDIR-} == xyes ]; then
+    ${FLATPAK} --system remote-modify --title=NewTitle test-repo
+    ${FLATPAK} remotes -d | grep ^test-repo > repo-info
+    assert_file_has_content repo-info "NewTitle"
+    ${FLATPAK} --system remote-modify --title=OldTitle test-repo
+
+    ${FLATPAK} remote-modify --title=NewTitle test-repo
+    ${FLATPAK} remotes -d | grep ^test-repo > repo-info
+    assert_file_has_content repo-info "NewTitle"
+    ${FLATPAK} --system remote-modify --title=OldTitle test-repo
+
+    if ${FLATPAK} --user remote-modify --title=NewTitle test-repo 2> remote-modify-error-log; then
+        assert_not_reached "flatpak --user remote-modify should not work for system remotes"
+    fi
+    assert_file_has_content remote-modify-error-log "Remote \"test-repo\" not found"
+else
+    ${FLATPAK} --user remote-modify --title=NewTitle test-repo
+    ${FLATPAK} remotes -d | grep ^test-repo > repo-info
+    assert_file_has_content repo-info "NewTitle"
+    ${FLATPAK} --user remote-modify --title=OldTitle test-repo
+
+    ${FLATPAK} remote-modify --title=NewTitle test-repo
+    ${FLATPAK} remotes -d | grep ^test-repo > repo-info
+    assert_file_has_content repo-info "NewTitle"
+    ${FLATPAK} remote-modify --title=OldTitle test-repo
+
+    if ${FLATPAK} --system remote-modify --title=NewTitle test-repo 2> remote-modify-error-log; then
+        assert_not_reached "flatpak --system remote-modify should not work for user remotes"
+    fi
+    assert_file_has_content remote-modify-error-log "Remote \"test-repo\" not found"
+fi
+
+echo "ok remote-modify"
+
+# Test that remote-delete works in all of the following cases:
+# * system remote, and --system is used
+# * system remote, and --system is omitted
+# * user remote, and --user is used
+# * user remote, and --user is omitted
+# and fails in the following cases:
+# * system remote, and --user is used
+# * user remote, and --system is used
+if [ x${USE_SYSTEMDIR-} == xyes ]; then
+    ${FLATPAK} --system remote-delete test-repo
+    ${FLATPAK} remotes > repo-info
+    assert_not_file_has_content repo-info "test-repo"
+    setup_repo
+
+    ${FLATPAK} remote-delete test-repo
+    ${FLATPAK} remotes > repo-list
+    assert_not_file_has_content repo-info "test-repo"
+    setup_repo
+
+    if ${FLATPAK} --user remote-delete test-repo 2> remote-delete-error-log; then
+        assert_not_reached "flatpak --user remote-delete should not work for system remotes"
+    fi
+    assert_file_has_content remote-delete-error-log "Remote \"test-repo\" not found"
+else
+    ${FLATPAK} --user remote-delete test-repo
+    ${FLATPAK} remotes > repo-info
+    assert_not_file_has_content repo-info "test-repo"
+    setup_repo
+
+    ${FLATPAK} remote-delete test-repo
+    ${FLATPAK} remotes > repo-info
+    assert_not_file_has_content repo-info "test-repo"
+    setup_repo
+
+    if ${FLATPAK} --system remote-delete test-repo 2> remote-delete-error-log; then
+        assert_not_reached "flatpak --system remote-delete should not work for user remotes"
+    fi
+    assert_file_has_content remote-delete-error-log "Remote \"test-repo\" not found"
+fi
+
+echo "ok remote-delete"
+
+# Test that remote-info works in all of the following cases:
+# * system remote, and --system is used
+# * system remote, and --system is omitted
+# * user remote, and --user is used
+# * user remote, and --user is omitted
+# and fails in the following cases:
+# * system remote, and --user is used
+# * user remote, and --system is used
+if [ x${USE_SYSTEMDIR-} == xyes ]; then
+    ${FLATPAK} --system remote-info test-repo org.test.Hello > remote-ref-info
+    assert_file_has_content remote-ref-info "ID: org.test.Hello"
+
+    ${FLATPAK} remote-info test-repo org.test.Hello > remote-ref-info
+    assert_file_has_content remote-ref-info "ID: org.test.Hello"
+
+    if ${FLATPAK} --user remote-info test-repo org.test.Hello 2> remote-info-error-log; then
+        assert_not_reached "flatpak --user remote-info should not work for system remotes"
+    fi
+    assert_file_has_content remote-info-error-log "Remote \"test-repo\" not found"
+else
+    ${FLATPAK} --user remote-info test-repo org.test.Hello > remote-ref-info
+    assert_file_has_content remote-ref-info "ID: org.test.Hello"
+
+    ${FLATPAK} remote-info test-repo org.test.Hello > remote-ref-info
+    assert_file_has_content remote-ref-info "ID: org.test.Hello"
+
+    if ${FLATPAK} --system remote-info test-repo org.test.Hello 2> remote-info-error-log; then
+        assert_not_reached "flatpak --system remote-info should not work for user remotes"
+    fi
+    assert_file_has_content remote-info-error-log "Remote \"test-repo\" not found"
+fi
+
+echo "ok remote-info"