diff --git a/services/pull/check.go b/services/pull/check.go
index 424d464d023..48ab332ed36 100644
--- a/services/pull/check.go
+++ b/services/pull/check.go
@@ -29,6 +29,7 @@ import (
 	"gitea.dev/modules/queue"
 	"gitea.dev/modules/setting"
 	"gitea.dev/modules/timeutil"
+	"gitea.dev/modules/util"
 	asymkey_service "gitea.dev/services/asymkey"
 	"gitea.dev/services/automergequeue"
 )
@@ -313,8 +314,7 @@ func getMergeCommit(ctx context.Context, pr *issues_model.PullRequest) (*git.Com
 	cmd := gitcmd.NewCommand("merge-base", "--is-ancestor").AddDynamicArguments(prHeadRef, pr.BaseBranch)
 	if err := cmd.WithRepo(pr.BaseRepo).RunWithStderr(ctx); err != nil {
 		if gitcmd.IsErrorExitCode(err, 1) {
-			// prHeadRef is not an ancestor of the base branch
-			return nil, nil //nolint:nilnil // return nil to indicate that the PR head is not merged
+			return nil, util.ErrNotExist // prHeadRef is not an ancestor of the base branch, no merge commit is found
 		}
 		// Errors are signaled by a non-zero status that is not 1
 		return nil, fmt.Errorf("%-v git merge-base --is-ancestor: %w", pr, err)
@@ -327,6 +327,9 @@ func getMergeCommit(ctx context.Context, pr *issues_model.PullRequest) (*git.Com
 	if err != nil {
 		return nil, fmt.Errorf("GetFullCommitID(%s) in %s: %w", prHeadRef, pr.BaseRepo.FullName(), err)
 	}
+	if prHeadCommitID == pr.MergeBase {
+		return nil, util.ErrNotExist // empty PR, no merge commit is found
+	}
 
 	gitRepo, err := git.OpenRepository(ctx, pr.BaseRepo)
 	if err != nil {
@@ -403,13 +406,10 @@ func manuallyMergedByPushedCommit(ctx context.Context, pr *issues_model.PullRequ
 	}
 
 	commit, err := getMergeCommit(ctx, pr)
-	if err != nil {
-		log.Error("%-v getMergeCommit: %v", pr, err)
+	if errors.Is(err, util.ErrNotExist) {
 		return false
-	}
-
-	if commit == nil {
-		// no merge commit found
+	} else if err != nil {
+		log.Error("%-v getMergeCommit: %v", pr, err)
 		return false
 	}
 
diff --git a/tests/integration/manual_merge_test.go b/tests/integration/manual_merge_test.go
index ae94101844a..cf6781a1e9a 100644
--- a/tests/integration/manual_merge_test.go
+++ b/tests/integration/manual_merge_test.go
@@ -5,6 +5,7 @@ package integration
 
 import (
 	"fmt"
+	"net/http"
 	"net/url"
 	"strings"
 	"testing"
@@ -16,6 +17,7 @@ import (
 	"gitea.dev/models/unittest"
 	user_model "gitea.dev/models/user"
 	"gitea.dev/modules/git/gitcmd"
+	"gitea.dev/modules/queue"
 	"gitea.dev/modules/setting"
 	api "gitea.dev/modules/structs"
 
@@ -59,6 +61,10 @@ func TestManualMergeAutodetect(t *testing.T) {
 			require.NoError(t, err)
 		}
 
+		testAPICreateBranch(t, user2Ctx.Session, user2.Name, repoName, defaultBranch, "empty-pr", http.StatusCreated)
+		emptyAPIPull, err := doAPICreatePullRequest(user1Ctx, user2.Name, repoName, defaultBranch, "empty-pr")(t)
+		require.NoError(t, err)
+
 		// user1 clones, then merges every branch sequentially, then pushes once.
 		// The first merge fast-forwards; the rest produce real merge commits,
 		// which generates multiple commits for "git rev-list --ancestry-path --merges ...".
@@ -100,5 +106,10 @@ func TestManualMergeAutodetect(t *testing.T) {
 			assert.Equalf(t, user1.ID, pr.MergerID, "PR %d (%s) merger should be the pusher", i+1, branchNames[i])
 			assert.Equalf(t, expectedMergeCommits[i], pr.MergedCommitID, "PR %d (%s) should be attributed to its own merge commit, not another PR's", i+1, branchNames[i])
 		}
+
+		require.NoError(t, queue.GetManager().FlushAll(t.Context(), 5*time.Second))
+		emptyPR := unittest.AssertExistsAndLoadBean(t, &issues_model.PullRequest{ID: emptyAPIPull.ID})
+		assert.False(t, emptyPR.HasMerged, "empty PR must not be detected as manually merged")
+		assert.Equal(t, issues_model.PullRequestStatusAncestor, emptyPR.Status)
 	})
 }