diff --git a/src/workflow/ArcanistPatchWorkflow.php b/src/workflow/ArcanistPatchWorkflow.php
--- a/src/workflow/ArcanistPatchWorkflow.php
+++ b/src/workflow/ArcanistPatchWorkflow.php
@@ -307,6 +307,14 @@
         $repository_api->execxLocal('checkout -b %s', $branch_name);
       }
 
+      // Synchronize submodule state, since the checkout may have modified
+      // submodule references. See PHI1083.
+
+      // Note that newer versions of "git checkout" include a
+      // "--recurse-submodules" flag which accomplishes this goal a little
+      // more simply. For now, use the more compatible form.
+      $repository_api->execPassthru('submodule update --init --recursive');
+
       echo phutil_console_format(
         "%s\n",
         pht(
@@ -714,6 +722,24 @@
         throw new ArcanistUsageException(pht('Unable to apply patch!'));
       }
 
+      // See PHI1083 and PHI648. If the patch applied changes to submodules,
+      // it only updates the submodule pointer, not the actual submodule. We're
+      // left with the pointer update staged in the index, and the unmodified
+      // submodule on disk.
+
+      // If we then "git commit --all" or "git add --all", the unmodified
+      // submodule on disk is added to the index as a change, which effectively
+      // undoes the patch we just applied and reverts the submodule back to
+      // the previous state.
+
+      // To avoid this, do a submodule update before we continue.
+
+      // We could also possibly skip the "--all" flag so we don't have to do
+      // this submodule update, but we want to leave the working copy in a
+      // clean state anyway, so we're going to have to do an update at some
+      // point. This usually doesn't cost us anything.
+      $repository_api->execPassthru('submodule update --init --recursive');
+
       if ($this->shouldCommit()) {
         if ($bundle->getFullAuthor()) {
           $author_cmd = csprintf('--author=%s', $bundle->getFullAuthor());
@@ -735,14 +761,23 @@
       if ($this->canBranch() &&
           !$this->shouldBranch() &&
           $this->shouldCommit() && $has_base_revision) {
+
+        // See PHI1083 and PHI648. Synchronize submodule state after mutating
+        // the working copy.
+
         $repository_api->execxLocal('checkout %s', $original_branch);
+        $repository_api->execPassthru('submodule update --init --recursive');
+
         $ex = null;
         try {
           $repository_api->execxLocal('cherry-pick %s', $new_branch);
+          $repository_api->execPassthru('submodule update --init --recursive');
         } catch (Exception $ex) {
           // do nothing
         }
+
         $repository_api->execxLocal('branch -D %s', $new_branch);
+
         if ($ex) {
           echo phutil_console_format(
             "\n<bg:red>** %s**</bg>\n",
@@ -751,11 +786,6 @@
         }
       }
 
-      // Synchronize submodule state, since the patch may have made changes
-      // to ".gitmodules". We do this after we finish managing branches so
-      // the behavior is correct under "--nobranch"; see PHI648.
-      $repository_api->execPassthru('submodule update --init --recursive');
-
       echo phutil_console_format(
         "<bg:green>** %s **</bg> %s\n",
         pht('OKAY'),