diff --git a/integrations/pull_merge_test.go b/integrations/pull_merge_test.go
index 218f0e4da66..5a9283edcfa 100644
--- a/integrations/pull_merge_test.go
+++ b/integrations/pull_merge_test.go
@@ -105,8 +105,6 @@ func TestPullRebase(t *testing.T) {
 
 func TestPullRebaseMerge(t *testing.T) {
 	onGiteaRun(t, func(t *testing.T, giteaURL *url.URL) {
-		defer prepareTestEnv(t)()
-
 		hookTasks, err := models.HookTasks(1, 1) //Retrieve previous hook number
 		assert.NoError(t, err)
 		hookTasksLenBefore := len(hookTasks)
@@ -129,8 +127,6 @@ func TestPullRebaseMerge(t *testing.T) {
 
 func TestPullSquash(t *testing.T) {
 	onGiteaRun(t, func(t *testing.T, giteaURL *url.URL) {
-		defer prepareTestEnv(t)()
-
 		hookTasks, err := models.HookTasks(1, 1) //Retrieve previous hook number
 		assert.NoError(t, err)
 		hookTasksLenBefore := len(hookTasks)
@@ -154,10 +150,9 @@ func TestPullSquash(t *testing.T) {
 
 func TestPullCleanUpAfterMerge(t *testing.T) {
 	onGiteaRun(t, func(t *testing.T, giteaURL *url.URL) {
-		defer prepareTestEnv(t)()
 		session := loginUser(t, "user1")
 		testRepoFork(t, session, "user2", "repo1", "user1", "repo1")
-		testEditFileToNewBranch(t, session, "user1", "repo1", "master", "feature/test", "README.md", "Hello, World (Edited)\n")
+		testEditFileToNewBranch(t, session, "user1", "repo1", "master", "feature/test", "README.md", "Hello, World (Edited - TestPullCleanUpAfterMerge)\n")
 
 		resp := testPullCreate(t, session, "user1", "repo1", "feature/test", "This is a pull title")
 
@@ -190,7 +185,6 @@ func TestPullCleanUpAfterMerge(t *testing.T) {
 
 func TestCantMergeWorkInProgress(t *testing.T) {
 	onGiteaRun(t, func(t *testing.T, giteaURL *url.URL) {
-		defer prepareTestEnv(t)()
 		session := loginUser(t, "user1")
 		testRepoFork(t, session, "user2", "repo1", "user1", "repo1")
 		testEditFile(t, session, "user1", "repo1", "master", "README.md", "Hello, World (Edited)\n")
@@ -212,7 +206,6 @@ func TestCantMergeWorkInProgress(t *testing.T) {
 
 func TestCantMergeConflict(t *testing.T) {
 	onGiteaRun(t, func(t *testing.T, giteaURL *url.URL) {
-		defer prepareTestEnv(t)()
 		session := loginUser(t, "user1")
 		testRepoFork(t, session, "user2", "repo1", "user1", "repo1")
 		testEditFileToNewBranch(t, session, "user1", "repo1", "master", "conflict", "README.md", "Hello, World (Edited Once)\n")
@@ -258,7 +251,6 @@ func TestCantMergeConflict(t *testing.T) {
 
 func TestCantMergeUnrelated(t *testing.T) {
 	onGiteaRun(t, func(t *testing.T, giteaURL *url.URL) {
-		defer prepareTestEnv(t)()
 		session := loginUser(t, "user1")
 		testRepoFork(t, session, "user2", "repo1", "user1", "repo1")
 		testEditFileToNewBranch(t, session, "user1", "repo1", "master", "base", "README.md", "Hello, World (Edited Twice)\n")
diff --git a/models/pull.go b/models/pull.go
index 9df5b90fc43..d165fde5f1b 100644
--- a/models/pull.go
+++ b/models/pull.go
@@ -649,44 +649,66 @@ func (pr *PullRequest) CheckUserAllowedToMerge(doer *User) (err error) {
 }
 
 // SetMerged sets a pull request to merged and closes the corresponding issue
-func (pr *PullRequest) SetMerged() (err error) {
+func (pr *PullRequest) SetMerged() (bool, error) {
 	if pr.HasMerged {
-		return fmt.Errorf("PullRequest[%d] already merged", pr.Index)
+		return false, fmt.Errorf("PullRequest[%d] already merged", pr.Index)
 	}
 	if pr.MergedCommitID == "" || pr.MergedUnix == 0 || pr.Merger == nil {
-		return fmt.Errorf("Unable to merge PullRequest[%d], some required fields are empty", pr.Index)
+		return false, fmt.Errorf("Unable to merge PullRequest[%d], some required fields are empty", pr.Index)
 	}
 
 	pr.HasMerged = true
 
 	sess := x.NewSession()
 	defer sess.Close()
-	if err = sess.Begin(); err != nil {
-		return err
+	if err := sess.Begin(); err != nil {
+		return false, err
 	}
 
-	if err = pr.loadIssue(sess); err != nil {
-		return err
+	if _, err := sess.Exec("UPDATE `issue` SET `repo_id` = `repo_id` WHERE `id` = ?", pr.IssueID); err != nil {
+		return false, err
 	}
 
-	if err = pr.Issue.loadRepo(sess); err != nil {
-		return err
-	}
-	if err = pr.Issue.Repo.getOwner(sess); err != nil {
-		return err
+	if _, err := sess.Exec("UPDATE `pull_request` SET `issue_id` = `issue_id` WHERE `id` = ?", pr.ID); err != nil {
+		return false, err
 	}
 
-	if _, err = pr.Issue.changeStatus(sess, pr.Merger, true); err != nil {
-		return fmt.Errorf("Issue.changeStatus: %v", err)
-	}
-	if _, err = sess.ID(pr.ID).Cols("has_merged, status, merged_commit_id, merger_id, merged_unix").Update(pr); err != nil {
-		return fmt.Errorf("update pull request: %v", err)
+	pr.Issue = nil
+	if err := pr.loadIssue(sess); err != nil {
+		return false, err
 	}
 
-	if err = sess.Commit(); err != nil {
-		return fmt.Errorf("Commit: %v", err)
+	if tmpPr, err := getPullRequestByID(sess, pr.ID); err != nil {
+		return false, err
+	} else if tmpPr.HasMerged {
+		if pr.Issue.IsClosed {
+			return false, nil
+		}
+		return false, fmt.Errorf("PullRequest[%d] already merged but it's associated issue [%d] is not closed", pr.Index, pr.IssueID)
+	} else if pr.Issue.IsClosed {
+		return false, fmt.Errorf("PullRequest[%d] already closed", pr.Index)
 	}
-	return nil
+
+	if err := pr.Issue.loadRepo(sess); err != nil {
+		return false, err
+	}
+
+	if err := pr.Issue.Repo.getOwner(sess); err != nil {
+		return false, err
+	}
+
+	if _, err := pr.Issue.changeStatus(sess, pr.Merger, true); err != nil {
+		return false, fmt.Errorf("Issue.changeStatus: %v", err)
+	}
+
+	if _, err := sess.Where("id = ?", pr.ID).Cols("has_merged, status, merged_commit_id, merger_id, merged_unix").Update(pr); err != nil {
+		return false, fmt.Errorf("Failed to update pr[%d]: %v", pr.ID, err)
+	}
+
+	if err := sess.Commit(); err != nil {
+		return false, fmt.Errorf("Commit: %v", err)
+	}
+	return true, nil
 }
 
 // NewPullRequest creates new pull request with labels for repository.
@@ -845,6 +867,12 @@ func (pr *PullRequest) UpdateCols(cols ...string) error {
 	return err
 }
 
+// UpdateColsIfNotMerged updates specific fields of a pull request if it has not been merged
+func (pr *PullRequest) UpdateColsIfNotMerged(cols ...string) error {
+	_, err := x.Where("id = ? AND has_merged = ?", pr.ID, false).Cols(cols...).Update(pr)
+	return err
+}
+
 // IsWorkInProgress determine if the Pull Request is a Work In Progress by its title
 func (pr *PullRequest) IsWorkInProgress() bool {
 	if err := pr.LoadIssue(); err != nil {
diff --git a/services/pull/check.go b/services/pull/check.go
index 055403d0df3..56561b7bbdd 100644
--- a/services/pull/check.go
+++ b/services/pull/check.go
@@ -31,7 +31,7 @@ var pullRequestQueue = sync.NewUniqueQueue(setting.Repository.PullRequestQueueLe
 func AddToTaskQueue(pr *models.PullRequest) {
 	go pullRequestQueue.AddFunc(pr.ID, func() {
 		pr.Status = models.PullRequestStatusChecking
-		if err := pr.UpdateCols("status"); err != nil {
+		if err := pr.UpdateColsIfNotMerged("status"); err != nil {
 			log.Error("AddToTaskQueue.UpdateCols[%d].(add to queue): %v", pr.ID, err)
 		}
 	})
@@ -142,9 +142,11 @@ func manuallyMerged(pr *models.PullRequest) bool {
 		pr.Merger = merger
 		pr.MergerID = merger.ID
 
-		if err = pr.SetMerged(); err != nil {
+		if merged, err := pr.SetMerged(); err != nil {
 			log.Error("PullRequest[%d].setMerged : %v", pr.ID, err)
 			return false
+		} else if !merged {
+			return false
 		}
 
 		baseGitRepo, err := git.OpenRepository(pr.BaseRepo.RepoPath())
@@ -194,7 +196,7 @@ func TestPullRequests(ctx context.Context) {
 			if err != nil {
 				log.Error("GetPullRequestByID[%s]: %v", prID, err)
 				continue
-			} else if pr.Status != models.PullRequestStatusChecking {
+			} else if pr.HasMerged {
 				continue
 			} else if manuallyMerged(pr) {
 				continue
diff --git a/services/pull/check_test.go b/services/pull/check_test.go
index 48a7774a612..043090249aa 100644
--- a/services/pull/check_test.go
+++ b/services/pull/check_test.go
@@ -18,7 +18,7 @@ import (
 func TestPullRequest_AddToTaskQueue(t *testing.T) {
 	assert.NoError(t, models.PrepareTestDatabase())
 
-	pr := models.AssertExistsAndLoadBean(t, &models.PullRequest{ID: 1}).(*models.PullRequest)
+	pr := models.AssertExistsAndLoadBean(t, &models.PullRequest{ID: 2}).(*models.PullRequest)
 	AddToTaskQueue(pr)
 
 	select {
@@ -29,6 +29,6 @@ func TestPullRequest_AddToTaskQueue(t *testing.T) {
 	}
 
 	assert.True(t, pullRequestQueue.Exist(pr.ID))
-	pr = models.AssertExistsAndLoadBean(t, &models.PullRequest{ID: 1}).(*models.PullRequest)
+	pr = models.AssertExistsAndLoadBean(t, &models.PullRequest{ID: 2}).(*models.PullRequest)
 	assert.Equal(t, models.PullRequestStatusChecking, pr.Status)
 }
diff --git a/services/pull/merge.go b/services/pull/merge.go
index 65a781e54ca..3958216b5ca 100644
--- a/services/pull/merge.go
+++ b/services/pull/merge.go
@@ -341,19 +341,30 @@ func Merge(pr *models.PullRequest, doer *models.User, baseGitRepo *git.Repositor
 	outbuf.Reset()
 	errbuf.Reset()
 
-	pr.MergedCommitID, err = baseGitRepo.GetBranchCommitID(pr.BaseBranch)
+	pr.MergedCommitID, err = git.GetFullCommitID(tmpBasePath, baseBranch)
 	if err != nil {
-		return fmt.Errorf("GetBranchCommit: %v", err)
+		return fmt.Errorf("Failed to get full commit id for the new merge: %v", err)
 	}
 
 	pr.MergedUnix = timeutil.TimeStampNow()
 	pr.Merger = doer
 	pr.MergerID = doer.ID
 
-	if err = pr.SetMerged(); err != nil {
+	if _, err = pr.SetMerged(); err != nil {
 		log.Error("setMerged [%d]: %v", pr.ID, err)
 	}
 
+	if err := pr.LoadIssue(); err != nil {
+		log.Error("loadIssue [%d]: %v", pr.ID, err)
+	}
+
+	if err := pr.Issue.LoadRepo(); err != nil {
+		log.Error("loadRepo for issue [%d]: %v", pr.ID, err)
+	}
+	if err := pr.Issue.Repo.GetOwner(); err != nil {
+		log.Error("GetOwner for issue repo [%d]: %v", pr.ID, err)
+	}
+
 	notification.NotifyMergePullRequest(pr, doer, baseGitRepo)
 
 	// Reset cached commit count