diff --git a/refs/files-backend.c b/refs/files-backend.c
index e029f5a885..8f3deddc71 100644
--- a/refs/files-backend.c
+++ b/refs/files-backend.c
@@ -1268,31 +1268,27 @@ static int files_pack_refs(struct ref_store *ref_store, unsigned int flags)
 static int files_delete_refs(struct ref_store *ref_store, const char *msg,
 			     struct string_list *refnames, unsigned int flags)
 {
-	struct files_ref_store *refs =
-		files_downcast(ref_store, REF_STORE_WRITE, "delete_refs");
+	struct ref_transaction *transaction;
 	struct strbuf err = STRBUF_INIT;
 	int i, result = 0;
 
 	if (!refnames->nr)
 		return 0;
 
-	if (packed_refs_lock(refs->packed_ref_store, 0, &err))
-		goto error;
-
-	if (refs_delete_refs(refs->packed_ref_store, msg, refnames, flags)) {
-		packed_refs_unlock(refs->packed_ref_store);
+	transaction = ref_store_transaction_begin(ref_store, &err);
+	if (!transaction)
 		goto error;
-	}
-
-	packed_refs_unlock(refs->packed_ref_store);
 
 	for (i = 0; i < refnames->nr; i++) {
 		const char *refname = refnames->items[i].string;
-
-		if (refs_delete_ref(&refs->base, msg, refname, NULL, flags))
+		if (ref_transaction_delete(transaction, refname, NULL,
+					   flags, msg, &err))
 			result |= error(_("could not remove reference %s"), refname);
 	}
+	if (ref_transaction_commit(transaction, &err))
+		goto error;
 
+	ref_transaction_free(transaction);
 	strbuf_release(&err);
 	return result;
 
@@ -1309,6 +1305,7 @@ static int files_delete_refs(struct ref_store *ref_store, const char *msg,
 	else
 		error(_("could not delete references: %s"), err.buf);
 
+	ref_transaction_free(transaction);
 	strbuf_release(&err);
 	return -1;
 }
diff --git a/refs/packed-backend.c b/refs/packed-backend.c
index 97b6837767..fdb7a0a52c 100644
--- a/refs/packed-backend.c
+++ b/refs/packed-backend.c
@@ -1519,55 +1519,6 @@ static int packed_initial_transaction_commit(struct ref_store *ref_store,
 	return ref_transaction_commit(transaction, err);
 }
 
-static int packed_delete_refs(struct ref_store *ref_store, const char *msg,
-			     struct string_list *refnames, unsigned int flags)
-{
-	struct packed_ref_store *refs =
-		packed_downcast(ref_store, REF_STORE_WRITE, "delete_refs");
-	struct strbuf err = STRBUF_INIT;
-	struct ref_transaction *transaction;
-	struct string_list_item *item;
-	int ret;
-
-	(void)refs; /* We need the check above, but don't use the variable */
-
-	if (!refnames->nr)
-		return 0;
-
-	/*
-	 * Since we don't check the references' old_oids, the
-	 * individual updates can't fail, so we can pack all of the
-	 * updates into a single transaction.
-	 */
-
-	transaction = ref_store_transaction_begin(ref_store, &err);
-	if (!transaction)
-		return -1;
-
-	for_each_string_list_item(item, refnames) {
-		if (ref_transaction_delete(transaction, item->string, NULL,
-					   flags, msg, &err)) {
-			warning(_("could not delete reference %s: %s"),
-				item->string, err.buf);
-			strbuf_reset(&err);
-		}
-	}
-
-	ret = ref_transaction_commit(transaction, &err);
-
-	if (ret) {
-		if (refnames->nr == 1)
-			error(_("could not delete reference %s: %s"),
-			      refnames->items[0].string, err.buf);
-		else
-			error(_("could not delete references: %s"), err.buf);
-	}
-
-	ref_transaction_free(transaction);
-	strbuf_release(&err);
-	return ret;
-}
-
 static int packed_pack_refs(struct ref_store *ref_store, unsigned int flags)
 {
 	/*
@@ -1595,7 +1546,7 @@ struct ref_storage_be refs_be_packed = {
 
 	.pack_refs = packed_pack_refs,
 	.create_symref = NULL,
-	.delete_refs = packed_delete_refs,
+	.delete_refs = NULL,
 	.rename_ref = NULL,
 	.copy_ref = NULL,
 
diff --git a/t/t1416-ref-transaction-hooks.sh b/t/t1416-ref-transaction-hooks.sh
index 77996017d7..3d39e1634a 100755
--- a/t/t1416-ref-transaction-hooks.sh
+++ b/t/t1416-ref-transaction-hooks.sh
@@ -789,39 +789,7 @@ test_expect_success "branch: rename branches" '
 	test_cmp_heads_and_tags -C workdir expect
 '
 
-# Mismatched hook output for "git branch -d":
-#
-#  * The delete branches operation should be treated as one transaction,
-#    but was splitted into several transactions on loose references,
-#    and the "reference-transaction committed" command was executed
-#    redundantly on the packed-ref-store.
-#
-# The differences are as follows:
-#
-#     @@ -2,11 +2,19 @@
-#      <ZERO-OID> <ZERO-OID> refs/heads/topic1
-#      <ZERO-OID> <ZERO-OID> refs/heads/topic2
-#      <ZERO-OID> <ZERO-OID> refs/heads/topic3
-#     +## Call hook: reference-transaction committed ##
-#     +<ZERO-OID> <ZERO-OID> refs/heads/topic1
-#     +<ZERO-OID> <ZERO-OID> refs/heads/topic2
-#     +<ZERO-OID> <ZERO-OID> refs/heads/topic3
-#     +## Call hook: reference-transaction  prepared ##
-#     +<ZERO-OID> <ZERO-OID> refs/heads/topic1
-#     +## Call hook: reference-transaction committed ##
-#     +<ZERO-OID> <ZERO-OID> refs/heads/topic1
-#      ## Call hook: reference-transaction  prepared ##
-#     -<COMMIT-A> <ZERO-OID> refs/heads/topic1
-#      <COMMIT-B> <ZERO-OID> refs/heads/topic2
-#     -<COMMIT-C> <ZERO-OID> refs/heads/topic3
-#      ## Call hook: reference-transaction committed ##
-#     -<COMMIT-A> <ZERO-OID> refs/heads/topic1
-#      <COMMIT-B> <ZERO-OID> refs/heads/topic2
-#     +## Call hook: reference-transaction  prepared ##
-#     +<COMMIT-C> <ZERO-OID> refs/heads/topic3
-#     +## Call hook: reference-transaction committed ##
-#      <COMMIT-C> <ZERO-OID> refs/heads/topic3
-test_expect_failure "branch: remove branches" '
+test_expect_success "branch: remove branches" '
 	test_when_finished "rm -f $HOOK_OUTPUT" &&
 
 	cat >expect <<-\EOF &&
@@ -950,39 +918,7 @@ test_expect_success "tag: update refs to create loose refs" '
 	test_cmp_heads_and_tags -C workdir expect
 '
 
-# Mismatched hook output for "git tag -d":
-#
-#  * The delete tags operation should be treated as one transaction,
-#    but was splitted into several transactions on loose references,
-#    and the "reference-transaction committed" command was executed
-#    redundantly on the packed-ref-store.
-#
-# The differences are as follows:
-#
-#     @@ -2,11 +2,19 @@
-#      <ZERO-OID> <ZERO-OID> refs/tags/v1
-#      <ZERO-OID> <ZERO-OID> refs/tags/v2
-#      <ZERO-OID> <ZERO-OID> refs/tags/v3
-#     +## Call hook: reference-transaction committed ##
-#     +<ZERO-OID> <ZERO-OID> refs/tags/v1
-#     +<ZERO-OID> <ZERO-OID> refs/tags/v2
-#     +<ZERO-OID> <ZERO-OID> refs/tags/v3
-#     +## Call hook: reference-transaction  prepared ##
-#     +<ZERO-OID> <ZERO-OID> refs/tags/v1
-#     +## Call hook: reference-transaction committed ##
-#     +<ZERO-OID> <ZERO-OID> refs/tags/v1
-#      ## Call hook: reference-transaction  prepared ##
-#     -<COMMIT-A> <ZERO-OID> refs/tags/v1
-#      <COMMIT-B> <ZERO-OID> refs/tags/v2
-#     -<COMMIT-C> <ZERO-OID> refs/tags/v3
-#      ## Call hook: reference-transaction committed ##
-#     -<COMMIT-A> <ZERO-OID> refs/tags/v1
-#      <COMMIT-B> <ZERO-OID> refs/tags/v2
-#     +## Call hook: reference-transaction  prepared ##
-#     +<COMMIT-C> <ZERO-OID> refs/tags/v3
-#     +## Call hook: reference-transaction committed ##
-#      <COMMIT-C> <ZERO-OID> refs/tags/v3
-test_expect_failure "tag: remove tags with mixed ref_stores" '
+test_expect_success "tag: remove tags with mixed ref_stores" '
 	test_when_finished "rm -f $HOOK_OUTPUT" &&
 
 	cat >expect <<-\EOF &&
diff --git a/t/t5510-fetch.sh b/t/t5510-fetch.sh
index b45879a760..dfdab09600 100755
--- a/t/t5510-fetch.sh
+++ b/t/t5510-fetch.sh
@@ -168,6 +168,8 @@ test_expect_success REFFILES 'fetch --prune fails to delete branches' '
 	cd "$D" &&
 	git clone . prune-fail &&
 	cd prune-fail &&
+	git update-ref refs/remotes/origin/extrabranch main~ &&
+	git pack-refs --all &&
 	git update-ref refs/remotes/origin/extrabranch main &&
 	: this will prevent --prune from locking packed-refs for deleting refs, but adding loose refs still succeeds  &&
 	>.git/packed-refs.new &&
@@ -175,6 +177,20 @@ test_expect_success REFFILES 'fetch --prune fails to delete branches' '
 	test_must_fail git fetch --prune origin
 '
 
+test_expect_success REFFILES 'fetch --prune ok for loose refs not in locked packed-refs' '
+	cd "$D" &&
+	git clone . prune-ok-ref-not-packed &&
+	(
+		cd prune-ok-ref-not-packed &&
+		git update-ref refs/remotes/origin/extrabranch main &&
+		: for loose refs not in packed-refs, we can delete them even the packed-refs is locked &&
+		:>.git/packed-refs.new &&
+
+		git fetch --prune origin &&
+		test_must_fail git rev-parse refs/remotes/origin/extrabranch --
+	)
+'
+
 test_expect_success 'fetch --atomic works with a single branch' '
 	test_when_finished "rm -rf \"$D\"/atomic" &&
 
