diff --git a/app/flatpak-builtins-uninstall.c b/app/flatpak-builtins-uninstall.c
index cf01305d8..2531411c8 100644
--- a/app/flatpak-builtins-uninstall.c
+++ b/app/flatpak-builtins-uninstall.c
@@ -49,79 +49,105 @@ static GOptionEntry options[] = {
   { NULL }
 };
 
+static gboolean
+looks_like_branch (const char *branch)
+{
+  /* In particular, / is not a valid branch char, so
+     this lets us distinguish full or partial refs as
+     non-branches. */
+  if (!flatpak_is_valid_branch (branch, NULL))
+    return FALSE;
+
+  /* Dots are allowed in branches, but not really used much, while
+     they are required for app ids, so thats a good check to
+     distinguish the two */
+  if (strchr (branch, '.') != NULL)
+    return FALSE;
+
+  return TRUE;
+}
+
 gboolean
 flatpak_builtin_uninstall (int argc, char **argv, GCancellable *cancellable, GError **error)
 {
   g_autoptr(GOptionContext) context = NULL;
   g_autoptr(FlatpakDir) dir = NULL;
-  const char *pref = NULL;
+  char **prefs = NULL;
+  int i, j, n_prefs;
   const char *default_branch = NULL;
   g_autofree char *ref = NULL;
   FlatpakHelperUninstallFlags flags = 0;
   g_autoptr(GPtrArray) related = NULL;
   FlatpakKinds kinds;
   FlatpakKinds kind;
-  g_autofree char *id = NULL;
-  g_autofree char *arch = NULL;
-  g_autofree char *branch = NULL;
-  int i;
+  g_autoptr(GHashTable) uninstall_refs_hash = NULL;
+  g_autoptr(GPtrArray) uninstall_refs = NULL;
 
-  context = g_option_context_new (_("NAME [BRANCH] - Uninstall an application"));
+  context = g_option_context_new (_("REF... - Uninstall an application"));
   g_option_context_set_translation_domain (context, GETTEXT_PACKAGE);
 
   if (!flatpak_option_context_parse (context, options, &argc, &argv, 0, &dir, cancellable, error))
     return FALSE;
 
   if (argc < 2)
-    return usage_error (context, _("NAME must be specified"), error);
+    return usage_error (context, _("Must specify at least one REF"), error);
 
-  if (argc > 3)
-    return usage_error (context, _("Too many arguments"), error);
+  prefs = &argv[1];
+  n_prefs = argc - 1;
 
-  pref = argv[1];
-  if (argc > 2)
-    default_branch = argv[2];
+  /* Backwards compat for old "REPOSITORY NAME [BRANCH]" argument version */
+  if (argc == 3 && looks_like_branch (argv[2]))
+    {
+      default_branch = argv[2];
+      n_prefs = 1;
+    }
 
   kinds = flatpak_kinds_from_bools (opt_app, opt_runtime);
+  uninstall_refs = g_ptr_array_new_with_free_func (g_free);
+  uninstall_refs_hash = g_hash_table_new_full (g_str_hash, g_str_equal, g_free, NULL);
 
-  if (!flatpak_split_partial_ref_arg (pref, kinds, opt_arch, default_branch,
-                                      &kinds, &id, &arch, &branch, error))
-    return FALSE;
-
-  ref = flatpak_dir_find_installed_ref (dir, id, branch, arch,
-                                        kinds, &kind, error);
-  if (ref == NULL)
-    return FALSE;
-
-  /* TODO: when removing runtimes, look for apps that use it, require --force */
-
-  if (opt_keep_ref)
-    flags |= FLATPAK_HELPER_UNINSTALL_FLAGS_KEEP_REF;
-  if (opt_force_remove)
-    flags |= FLATPAK_HELPER_UNINSTALL_FLAGS_FORCE_REMOVE;
-
-  if (!opt_no_related)
+  for (j = 0; j < n_prefs; j++)
     {
+      const char *pref = NULL;
+      FlatpakKinds matched_kinds;
+      g_autofree char *id = NULL;
+      g_autofree char *arch = NULL;
+      g_autofree char *branch = NULL;
       g_autoptr(GError) local_error = NULL;
       g_autofree char *origin = NULL;
 
+      pref = prefs[j];
+
+      if (!flatpak_split_partial_ref_arg (pref, kinds, opt_arch, default_branch,
+                                          &matched_kinds, &id, &arch, &branch, error))
+        return FALSE;
+
+      ref = flatpak_dir_find_installed_ref (dir, id, branch, arch,
+                                            kinds, &kind, error);
+      if (ref == NULL)
+        return FALSE;
+
+      if (g_hash_table_insert (uninstall_refs_hash, g_strdup (ref), NULL))
+        g_ptr_array_add (uninstall_refs, g_strdup (ref));
+
+      /* TODO: when removing runtimes, look for apps that use it, require --force */
+
+      if (opt_no_related)
+        continue;
+
       origin = flatpak_dir_get_origin (dir, ref, NULL, NULL);
-      if (origin)
+      if (origin == NULL)
+        continue;
+
+      related = flatpak_dir_find_local_related (dir, ref, origin,
+                                                NULL, &local_error);
+      if (related == NULL)
         {
-          related = flatpak_dir_find_local_related (dir, ref, origin,
-                                                    NULL, &local_error);
-          if (related == NULL)
-            g_printerr (_("Warning: Problem looking for related refs: %s\n"),
-                        local_error->message);
+          g_printerr (_("Warning: Problem looking for related refs: %s\n"),
+                      local_error->message);
+          continue;
         }
-    }
 
-  if (!flatpak_dir_uninstall (dir, ref, flags,
-                              cancellable, error))
-    return FALSE;
-
-  if (related != NULL)
-    {
       for (i = 0; i < related->len; i++)
         {
           FlatpakRelated *rel = g_ptr_array_index (related, i);
@@ -132,15 +158,26 @@ flatpak_builtin_uninstall (int argc, char **argv, GCancellable *cancellable, GEr
             continue;
 
           parts = g_strsplit (rel->ref, "/", 0);
-          g_print (_("Uninstalling related: %s\n"), parts[1]);
 
-          if (!flatpak_dir_uninstall (dir, rel->ref, flags,
-                                      cancellable, &local_error))
-            g_printerr (_("Warning: Failed to uninstall related ref: %s\n"),
-                        rel->ref);
+          if (g_hash_table_insert (uninstall_refs_hash, g_strdup (rel->ref), NULL))
+            g_ptr_array_add (uninstall_refs, g_strdup (rel->ref));
         }
     }
 
+  if (opt_keep_ref)
+    flags |= FLATPAK_HELPER_UNINSTALL_FLAGS_KEEP_REF;
+  if (opt_force_remove)
+    flags |= FLATPAK_HELPER_UNINSTALL_FLAGS_FORCE_REMOVE;
+
+  for (i = 0; i < uninstall_refs->len; i++)
+    {
+      const char *ref = (char *)g_ptr_array_index (uninstall_refs, i);
+      g_print ("uninstalling %s\n", ref);
+      if (!flatpak_dir_uninstall (dir, ref, flags,
+                                  cancellable, error))
+        return FALSE;
+    }
+
   return TRUE;
 }
 
@@ -152,7 +189,6 @@ flatpak_complete_uninstall (FlatpakCompletion *completion)
   g_autoptr(GError) error = NULL;
   g_auto(GStrv) refs = NULL;
   FlatpakKinds kinds;
-  int i;
 
   context = g_option_context_new ("");
   if (!flatpak_option_context_parse (context, options, &completion->argc, &completion->argv, 0, &dir, NULL, NULL))
@@ -163,37 +199,11 @@ flatpak_complete_uninstall (FlatpakCompletion *completion)
   switch (completion->argc)
     {
     case 0:
-    case 1: /* NAME */
+    default: /* REF */
       flatpak_complete_options (completion, global_entries);
       flatpak_complete_options (completion, options);
       flatpak_complete_options (completion, user_entries);
-
-      refs = flatpak_dir_find_installed_refs (dir, NULL, NULL, opt_arch,
-                                              kinds, &error);
-      if (refs == NULL)
-        flatpak_completion_debug ("find installed refs error: %s", error->message);
-      for (i = 0; refs != NULL && refs[i] != NULL; i++)
-        {
-          g_auto(GStrv) parts = flatpak_decompose_ref (refs[i], NULL);
-          if (parts)
-            flatpak_complete_word (completion, "%s ", parts[1]);
-        }
-      break;
-
-    case 2: /* Branch */
-      refs = flatpak_dir_find_installed_refs (dir, completion->argv[1], NULL, opt_arch,
-                                              kinds, &error);
-      if (refs == NULL)
-        flatpak_completion_debug ("find installed refs error: %s", error->message);
-      for (i = 0; refs != NULL && refs[i] != NULL; i++)
-        {
-          g_auto(GStrv) parts = flatpak_decompose_ref (refs[i], NULL);
-          if (parts)
-            flatpak_complete_word (completion, "%s ", parts[3]);
-        }
-      break;
-
-    default:
+      flatpak_complete_partial_ref (completion, kinds, opt_arch, dir, NULL);
       break;
     }
 
diff --git a/doc/flatpak-uninstall.xml b/doc/flatpak-uninstall.xml
index 6d715549f..e3f4c17ef 100644
--- a/doc/flatpak-uninstall.xml
+++ b/doc/flatpak-uninstall.xml
@@ -32,8 +32,7 @@
             <cmdsynopsis>
                 <command>flatpak uninstall</command>
                 <arg choice="opt" rep="repeat">OPTION</arg>
-                <arg choice="plain">NAME</arg>
-                <arg choice="opt">BRANCH</arg>
+                <arg choice="opt" rep="repeat">REF</arg>
             </cmdsynopsis>
     </refsynopsisdiv>
 
@@ -41,12 +40,17 @@
         <title>Description</title>
 
         <para>
-            Uninstalls an application or runtime. The <arg choice="plain">NAME</arg>,
-            <arg choice="plain">ARCH</arg> and <arg choice="plain">BRANCH</arg>
-            arguments must identify an installed application.
-            If <arg choice="plain">BRANCH</arg> is not specified, it defaults
-            to whatever is installed, unless there are multiple versions, then you
-            have to specify a branch.
+            Uninstalls an application or runtime. <arg choice="plain">REF</arg> is a reference to the
+            application or runtime to install. If no <arg choice="plain">REF</arg> is given, everything
+            is updated.
+        </para>
+        <para>
+            Each <arg choice="plain">REF</arg> arguments is a full or partial indentifier in the
+            flatpak ref format, which looks like "(app|runtime)/ID/ARCH/BRANCH". All elements
+            except ID are optional and can be left out, including the slashes,
+            so most of the time you need only specify ID. Any part left out will be matched
+            against what is installed, and if there are multiple matches an error message
+            will list the alternatives.
         </para>
         <para>
             By default this looks for both installed apps and runtime