diff --git a/models/issues/issue_xref.go b/models/issues/issue_xref.go
index 74f97f1ad51..09865bda0d0 100644
--- a/models/issues/issue_xref.go
+++ b/models/issues/issue_xref.go
@@ -10,6 +10,7 @@ import (
 	"gitea.dev/models/db"
 	access_model "gitea.dev/models/perm/access"
 	repo_model "gitea.dev/models/repo"
+	"gitea.dev/models/unit"
 	user_model "gitea.dev/models/user"
 	"gitea.dev/modules/log"
 	"gitea.dev/modules/references"
@@ -202,8 +203,13 @@ func (issue *Issue) verifyReferencedIssue(stdCtx context.Context, ctx *crossRefe
 		return nil, references.XRefActionNone, err
 	}
 
-	// Close/reopen actions can only be set from pull requests to issues
-	if refIssue.IsPull || !issue.IsPull {
+	// Close/reopen actions can only be set from pull requests, reopen only to issues
+	if !issue.IsPull || (refIssue.IsPull && refAction == references.XRefActionReopens) {
+		refAction = references.XRefActionNone
+	}
+
+	// With an external tracker, pull requests are referenced as "!N"
+	if refAction != references.XRefActionNone && !ref.IsPull && refIssue.IsPull && refIssue.Repo.UnitEnabled(stdCtx, unit.TypeExternalTracker) {
 		refAction = references.XRefActionNone
 	}
 
diff --git a/models/issues/issue_xref_test.go b/models/issues/issue_xref_test.go
index 4ecc6547852..6c66e11af0a 100644
--- a/models/issues/issue_xref_test.go
+++ b/models/issues/issue_xref_test.go
@@ -10,6 +10,7 @@ import (
 	"gitea.dev/models/db"
 	issues_model "gitea.dev/models/issues"
 	repo_model "gitea.dev/models/repo"
+	"gitea.dev/models/unit"
 	"gitea.dev/models/unittest"
 	user_model "gitea.dev/models/user"
 	"gitea.dev/modules/references"
@@ -24,22 +25,26 @@ func TestXRef_AddCrossReferences(t *testing.T) {
 	itarget := testCreateIssue(t, 1, 2, "title1", "content1", false)
 
 	// PR to close issue #1
-	content := fmt.Sprintf("content2, closes #%d", itarget.Index)
+	content := fmt.Sprintf("content2, closes #%d, fixes #2", itarget.Index)
 	pr := testCreateIssue(t, 1, 2, "title2", content, true)
 	ref := unittest.AssertExistsAndLoadBean(t, &issues_model.Comment{IssueID: itarget.ID, RefIssueID: pr.ID, RefCommentID: 0})
 	assert.Equal(t, issues_model.CommentTypePullRef, ref.Type)
 	assert.Equal(t, pr.RepoID, ref.RefRepoID)
 	assert.True(t, ref.RefIsPull)
 	assert.Equal(t, references.XRefActionCloses, ref.RefAction)
+	ref = unittest.AssertExistsAndLoadBean(t, &issues_model.Comment{IssueID: 2, RefIssueID: pr.ID, RefCommentID: 0})
+	assert.Equal(t, references.XRefActionCloses, ref.RefAction)
 
 	// Comment on PR to reopen issue #1
-	content = fmt.Sprintf("content2, reopens #%d", itarget.Index)
+	content = fmt.Sprintf("content2, reopens #%d, reopens #2", itarget.Index)
 	c := testCreateComment(t, 2, pr.ID, content)
 	ref = unittest.AssertExistsAndLoadBean(t, &issues_model.Comment{IssueID: itarget.ID, RefIssueID: pr.ID, RefCommentID: c.ID})
 	assert.Equal(t, issues_model.CommentTypeCommentRef, ref.Type)
 	assert.Equal(t, pr.RepoID, ref.RefRepoID)
 	assert.True(t, ref.RefIsPull)
 	assert.Equal(t, references.XRefActionReopens, ref.RefAction)
+	ref = unittest.AssertExistsAndLoadBean(t, &issues_model.Comment{IssueID: 2, RefIssueID: pr.ID, RefCommentID: c.ID})
+	assert.Equal(t, references.XRefActionNone, ref.RefAction)
 
 	// Issue mentioning issue #1
 	content = fmt.Sprintf("content3, mentions #%d", itarget.Index)
@@ -66,6 +71,14 @@ func TestXRef_AddCrossReferences(t *testing.T) {
 	content = fmt.Sprintf("content6, mentions org3/repo3#%d", itarget.Index)
 	i = testCreateIssue(t, 4, 5, "title6", content, false)
 	unittest.AssertNotExistsBean(t, &issues_model.Comment{IssueID: itarget.ID, RefIssueID: i.ID, RefCommentID: 0})
+
+	assert.NoError(t, db.DeleteBeans(t.Context(), &repo_model.RepoUnit{RepoID: 1, Type: unit.TypeIssues}))
+	assert.NoError(t, db.Insert(t.Context(), &repo_model.RepoUnit{RepoID: 1, Type: unit.TypeExternalTracker, Config: &repo_model.ExternalTrackerConfig{}}))
+	c = testCreateComment(t, 2, pr.ID, "fixes #2, fixes !3")
+	ref = unittest.AssertExistsAndLoadBean(t, &issues_model.Comment{IssueID: 2, RefIssueID: pr.ID, RefCommentID: c.ID})
+	assert.Equal(t, references.XRefActionNone, ref.RefAction)
+	ref = unittest.AssertExistsAndLoadBean(t, &issues_model.Comment{IssueID: 3, RefIssueID: pr.ID, RefCommentID: c.ID})
+	assert.Equal(t, references.XRefActionCloses, ref.RefAction)
 }
 
 func TestXRef_NeuterCrossReferences(t *testing.T) {
diff --git a/modules/references/references.go b/modules/references/references.go
index 0d470d479ae..db8f9d606dd 100644
--- a/modules/references/references.go
+++ b/modules/references/references.go
@@ -85,6 +85,7 @@ type IssueReference struct {
 	Index   int64
 	Owner   string
 	Name    string
+	IsPull  bool
 	Action  XRefAction
 	TimeLog string
 }
@@ -123,6 +124,7 @@ func rawToIssueReferenceList(reflist []*rawReference) []IssueReference {
 			Index:   r.index,
 			Owner:   r.owner,
 			Name:    r.name,
+			IsPull:  r.isPull,
 			Action:  r.action,
 			TimeLog: r.timeLog,
 		}
diff --git a/services/issue/commit.go b/services/issue/commit.go
index 0fb070d0c17..1847979f7ce 100644
--- a/services/issue/commit.go
+++ b/services/issue/commit.go
@@ -18,6 +18,7 @@ import (
 	issues_model "gitea.dev/models/issues"
 	access_model "gitea.dev/models/perm/access"
 	repo_model "gitea.dev/models/repo"
+	"gitea.dev/models/unit"
 	user_model "gitea.dev/models/user"
 	"gitea.dev/modules/container"
 	"gitea.dev/modules/git"
@@ -188,8 +189,8 @@ func UpdateIssuesCommit(ctx context.Context, doer *user_model.User, repo *repo_m
 				return err
 			}
 
-			// Only issues can be closed/reopened this way, and user needs the correct permissions
-			if refIssue.IsPull || !canclose {
+			// Only issues can be reopened this way, and user needs the correct permissions
+			if !canclose || (refIssue.IsPull && ref.Action == references.XRefActionReopens) {
 				continue
 			}
 
@@ -198,6 +199,11 @@ func UpdateIssuesCommit(ctx context.Context, doer *user_model.User, repo *repo_m
 				continue
 			}
 
+			// With an external tracker, pull requests are referenced as "!N"
+			if !ref.IsPull && refIssue.IsPull && refRepo.UnitEnabled(ctx, unit.TypeExternalTracker) {
+				continue
+			}
+
 			if !repo.CloseIssuesViaCommitInAnyBranch {
 				// If the issue was specified to be in a particular branch, don't allow commits in other branches to close it
 				if refIssue.Ref != "" {
diff --git a/services/issue/commit_test.go b/services/issue/commit_test.go
index 61e4b00cb21..3c7d753c886 100644
--- a/services/issue/commit_test.go
+++ b/services/issue/commit_test.go
@@ -42,7 +42,7 @@ func TestUpdateIssuesCommit(t *testing.T) {
 			CommitterName:  "User Two",
 			AuthorEmail:    "user2@example.com",
 			AuthorName:     "User Two",
-			Message:        "close #2",
+			Message:        "close #2, reopen #2",
 		},
 	}
 
@@ -56,7 +56,7 @@ func TestUpdateIssuesCommit(t *testing.T) {
 		PosterID:  user.ID,
 		IssueID:   1,
 	}
-	issueBean := &issues_model.Issue{RepoID: repo.ID, Index: 4}
+	issueBean := &issues_model.Issue{RepoID: repo.ID, Index: 2}
 
 	unittest.AssertNotExistsBean(t, commentBean)
 	unittest.AssertNotExistsBean(t, &issues_model.Issue{RepoID: repo.ID, Index: 2}, "is_closed=1")
@@ -117,6 +117,13 @@ func TestUpdateIssuesCommit(t *testing.T) {
 	unittest.AssertExistsAndLoadBean(t, commentBean)
 	unittest.AssertExistsAndLoadBean(t, issueBean, "is_closed=1")
 	unittest.CheckConsistencyFor(t, &activities_model.Action{})
+
+	repo = unittest.AssertExistsAndLoadBean(t, &repo_model.Repository{ID: 48})
+	admin := unittest.AssertExistsAndLoadBean(t, &user_model.User{ID: 1})
+	assert.NoError(t, UpdateIssuesCommit(t.Context(), admin, repo, []*repository.PushCommit{{Sha1: "abcdef4", Message: "close #1"}}, repo.DefaultBranch))
+	unittest.AssertExistsAndLoadBean(t, &issues_model.Issue{RepoID: repo.ID, Index: 1}, "is_closed=0")
+	assert.NoError(t, UpdateIssuesCommit(t.Context(), admin, repo, []*repository.PushCommit{{Sha1: "abcdef5", Message: "close !1"}}, repo.DefaultBranch))
+	unittest.AssertExistsAndLoadBean(t, &issues_model.Issue{RepoID: repo.ID, Index: 1}, "is_closed=1")
 }
 
 func TestUpdateIssuesCommit_Colon(t *testing.T) {