diff --git a/airflow-core/newsfragments/68954.bugfix.rst b/airflow-core/newsfragments/68954.bugfix.rst
new file mode 100644
index 0000000000000..eca1675dadfe4
--- /dev/null
+++ b/airflow-core/newsfragments/68954.bugfix.rst
@@ -0,0 +1 @@
+Fix branch operators not skipping mapped or cleared downstream tasks when a custom XCom backend is configured.
diff --git a/airflow-core/tests/unit/ti_deps/deps/test_not_previously_skipped_dep.py b/airflow-core/tests/unit/ti_deps/deps/test_not_previously_skipped_dep.py
index 58ccce35dd896..cd5b364311bce 100644
--- a/airflow-core/tests/unit/ti_deps/deps/test_not_previously_skipped_dep.py
+++ b/airflow-core/tests/unit/ti_deps/deps/test_not_previously_skipped_dep.py
@@ -17,14 +17,17 @@
 # under the License.
 from __future__ import annotations
 
+from unittest import mock
+
 import pendulum
 import pytest
-from sqlalchemy import delete
+from sqlalchemy import delete, select
 
 from airflow.models import DagRun, TaskInstance
 from airflow.models.xcom import XComModel
 from airflow.providers.standard.operators.empty import EmptyOperator
 from airflow.providers.standard.operators.python import BranchPythonOperator
+from airflow.sdk.bases.xcom import BaseXCom
 from airflow.ti_deps.dep_context import DepContext
 from airflow.ti_deps.deps.not_previously_skipped_dep import (
     XCOM_SKIPMIXIN_FOLLOWED,
@@ -214,3 +217,65 @@ def test_unmapped_parent_skip_mapped_downstream(session, dag_maker):
     assert len(list(dep.get_dep_statuses(tis["op2"], DepContext(), session=session))) == 1
     assert not dep.is_met(tis["op2"], session=session)
     assert tis["op2"].state == State.SKIPPED
+
+
+def test_branch_skip_decision_bypasses_custom_xcom_backend(session, dag_maker):
+    """
+    A value-externalizing custom XCom backend must not break branch-skip of
+    mapped/cleared downstream tasks.
+
+    The branch decision is written through the real worker push path with such a
+    backend configured. It must be stored readably (not as the backend's opaque
+    pointer) so that NotPreviouslySkippedDep can skip a not-yet-expanded mapped
+    downstream task, which the worker does not skip directly.
+
+    Regression test for https://github.com/apache/airflow/issues/50491.
+    """
+
+    class _PointerXComBackend(BaseXCom):
+        @staticmethod
+        def serialize_value(value, **kwargs):
+            return "xcom_s3://pointer"
+
+        @staticmethod
+        def deserialize_value(result):
+            return "xcom_s3://pointer"
+
+    start_date = pendulum.datetime(2020, 1, 1)
+    with dag_maker(
+        "test_skip_bypass_backend_dag",
+        schedule=None,
+        start_date=start_date,
+        session=session,
+    ):
+        op1 = BranchPythonOperator(task_id="op1", python_callable=lambda: "op3")
+        op2 = EmptyOperator(task_id="op2")
+        op3 = EmptyOperator(task_id="op3")
+        op1 >> [op2, op3]
+
+    dr = dag_maker.create_dagrun(run_type=DagRunType.MANUAL, state=State.RUNNING)
+    tis = {ti.task_id: ti for ti in dr.task_instances}
+
+    with mock.patch("airflow.sdk.execution_time.task_runner.XCom", _PointerXComBackend):
+        run_task_instance(tis["op1"], op1)
+
+    stored = session.scalar(
+        select(XComModel.value).where(
+            XComModel.dag_id == dr.dag_id,
+            XComModel.task_id == "op1",
+            XComModel.run_id == dr.run_id,
+            XComModel.key == XCOM_SKIPMIXIN_KEY,
+            XComModel.map_index == -1,
+        )
+    )
+
+    assert stored is not None
+    assert "xcom_s3://pointer" not in str(stored)
+
+    tis["op2"].map_index = 0
+    session.merge(tis["op2"])
+    session.flush()
+
+    dep = NotPreviouslySkippedDep()
+    assert len(list(dep.get_dep_statuses(tis["op2"], DepContext(), session=session))) == 1
+    assert tis["op2"].state == State.SKIPPED
diff --git a/task-sdk/src/airflow/sdk/execution_time/task_runner.py b/task-sdk/src/airflow/sdk/execution_time/task_runner.py
index f3fee689928a0..f941d6a5d60dd 100644
--- a/task-sdk/src/airflow/sdk/execution_time/task_runner.py
+++ b/task-sdk/src/airflow/sdk/execution_time/task_runner.py
@@ -57,6 +57,7 @@
     TIRunContext,
 )
 from airflow.sdk.bases.operator import BaseOperator, ExecutorSafeguard
+from airflow.sdk.bases.skipmixin import XCOM_SKIPMIXIN_KEY
 from airflow.sdk.bases.xcom import BaseXCom
 from airflow.sdk.configuration import conf
 from airflow.sdk.definitions._internal.dag_parsing_context import _airflow_parsing_context_manager
@@ -880,6 +881,14 @@ def _xcom_push(
     # Private function, as we don't want to expose the ability to manually set `mapped_length` to SDK
     # consumers
 
+    if key == XCOM_SKIPMIXIN_KEY:
+        # The branch/skip decision is control-plane data the scheduler reads (via
+        # NotPreviouslySkippedDep) to skip mapped or cleared downstream tasks. It must
+        # bypass any custom XCom backend, which could externalize it into a pointer the
+        # scheduler cannot interpret, silently leaving those tasks unskipped (#50491).
+        _xcom_push_to_db(ti, key, value)
+        return
+
     XCom.set(
         key=key,
         value=value,