diff --git a/server/events/working_dir.go b/server/events/working_dir.go
index aab1fb83e8..1a65c588b6 100644
--- a/server/events/working_dir.go
+++ b/server/events/working_dir.go
@@ -117,11 +117,15 @@ func (w *FileWorkspace) Clone(
 		// We're prefix matching here because BitBucket doesn't give us the full
 		// commit, only a 12 character prefix.
 		if strings.HasPrefix(currCommit, p.HeadCommit) {
-			log.Debug("repo is at correct commit %q so will not re-clone", p.HeadCommit)
-			return cloneDir, w.warnDiverged(log, p, headRepo, cloneDir), nil
+			if w.CheckoutMerge && w.recheckDiverged(log, p, headRepo, cloneDir) {
+				log.Info("base branch has been updated, using merge strategy and will clone again")
+			} else {
+				log.Debug("repo is at correct commit %q so will not re-clone", p.HeadCommit)
+				return cloneDir, false, nil
+			}
+		} else {
+			log.Debug("repo was already cloned but is not at correct commit, wanted %q got %q", p.HeadCommit, currCommit)
 		}
-
-		log.Debug("repo was already cloned but is not at correct commit, wanted %q got %q", p.HeadCommit, currCommit)
 		// We'll fall through to re-clone.
 	}
 
@@ -129,14 +133,14 @@ func (w *FileWorkspace) Clone(
 	return cloneDir, false, w.forceClone(log, cloneDir, headRepo, p)
 }
 
-// warnDiverged returns true if we should warn the user that the branch we're
-// merging into has diverged from what we currently have checked out.
+// recheckDiverged returns true if the branch we're merging into has diverged
+// from what we currently have checked out.
 // This matters in the case of the merge checkout strategy because after
-// cloning the repo and doing the merge, it's possible main was updated.
-// Then users won't be getting the merge functionality they expected.
+// cloning the repo and doing the merge, it's possible main was updated
+// and we have to perform a new merge.
 // If there are any errors we return false since we prefer things to succeed
 // vs. stopping the plan/apply.
-func (w *FileWorkspace) warnDiverged(log logging.SimpleLogging, p models.PullRequest, headRepo models.Repo, cloneDir string) bool {
+func (w *FileWorkspace) recheckDiverged(log logging.SimpleLogging, p models.PullRequest, headRepo models.Repo, cloneDir string) bool {
 	if !w.CheckoutMerge {
 		// It only makes sense to warn that main has diverged if we're using
 		// the checkout merge strategy. If we're just checking out the branch,
@@ -174,13 +178,7 @@ func (w *FileWorkspace) warnDiverged(log logging.SimpleLogging, p models.PullReq
 		}
 	}
 
-	hasDiverged := w.HasDiverged(log, cloneDir)
-	if hasDiverged {
-		log.Info("remote main branch is ahead and thereby has new commits, it is recommended to pull new commits")
-	} else {
-		log.Debug("remote main branch has no new commits")
-	}
-	return hasDiverged
+	return w.HasDiverged(log, cloneDir)
 }
 
 func (w *FileWorkspace) HasDiverged(log logging.SimpleLogging, cloneDir string) bool {