diff --git a/.github/workflows/README.md b/.github/workflows/README.md
index e0afce047bf..619e99f8b72 100644
--- a/.github/workflows/README.md
+++ b/.github/workflows/README.md
@@ -171,13 +171,26 @@ safe to make a required check.
 
 ### Label events
 
-`ci.yml` also fires on `pull_request.types: [labeled]`, so applying
-`run-spark-3.4-tests`, `run-spark-4.0-tests` or `run-iceberg-tests` starts the
-job that label gates without needing a new push. GitHub cannot filter a
-`pull_request` trigger by label name, so **every** label added to a PR starts a
-run, including labels that gate nothing.
-
-Two rules keep those runs from corrupting the PR's status:
+`ci_label.yml` fires on `pull_request.types: [labeled]` and calls `ci.yml`
+through `workflow_call`, so applying `run-spark-3.4-tests`,
+`run-spark-4.0-tests` or `run-iceberg-tests` starts the job that label gates
+without needing a new push. GitHub cannot filter a `pull_request` trigger by
+label name, so **every** label added to a PR starts a run, including labels
+that gate nothing. A called workflow sees its caller's event context, so
+`POLICY` still reads the `labeled` action and the label name.
+
+These rules keep those runs from corrupting the PR's status:
+
+- Label runs come from their own workflow, not from a `labeled` type on
+  `ci.yml`'s trigger. When one workflow runs twice at the same commit, GitHub
+  evaluates the PR's required checks against only one of the two runs. A PR
+  opened with a label already applied fires `opened` and `labeled` together,
+  and when GitHub picked the label run, `Required Checks` showed as "Expected"
+  forever and the merge queue never accepted the PR, see
+  [#6159](https://github.com/apache/datafusion-comet/issues/6159). A run of
+  `ci_label.yml` has its own check suite, and every check it publishes is
+  nested under its `Label run` job, so it cannot hide or replace a commit
+  run's check.
 
 - `preflight` and `changes` carry no event guard and run every time. A job held
   back by `if:` still publishes a check run under its own name with conclusion
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e4415959bd6..7f87d591995 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -62,18 +62,30 @@ name: Comet CI
 
 # A `labeled` event (e.g. the run-spark-*-tests gates, or dependabot's automatic
 # `dependencies` label added ~1s after open) fires at the same commit as the
-# opened/synchronize run. Keying the group on the label name keeps labeled runs
-# in their own subgroup so they never cancel the real commit run. Every other
-# run is keyed on its event name: opened, synchronize and reopened all map to
-# `pull_request`, so a new push still supersedes its predecessor, while a
-# scheduled run at the tip of main never cancels that commit's push run.
+# opened/synchronize run. Label runs reach this file through ci_label.yml, so
+# `github.workflow` already separates them from the commit run; keying the
+# group on the label name as well keeps two different labels from cancelling
+# each other. Every other run is keyed on its event name: opened, synchronize
+# and reopened all map to `pull_request`, so a new push still supersedes its
+# predecessor, while a scheduled run at the tip of main never cancels that
+# commit's push run.
 concurrency:
   group: ${{ github.repository }}-${{ github.head_ref || github.sha }}-${{ github.workflow }}-${{ github.event.action == 'labeled' && github.event.label.name || github.event_name }}
   cancel-in-progress: true
 
+# No `labeled` here: ci_label.yml handles that event and calls this file
+# through `workflow_call`. When one workflow runs twice at the same commit,
+# GitHub evaluates the pull request's required checks against only one of the
+# two runs. A PR opened with a label already applied gets both an `opened` and
+# a `labeled` run, and when the label run was the one GitHub picked, the
+# `Required Checks` context showed as "Expected" forever and the merge queue
+# never took the PR (issue #6159). A separate workflow gets its own check
+# suite, so a label run can never hide the commit run's verdict.
+# dev/ci/check-ci-config.py enforces this.
 on:
   pull_request:
-    types: [opened, synchronize, reopened, labeled]
+    types: [opened, synchronize, reopened]
+  workflow_call:
   merge_group:
   push:
     branches:
@@ -530,15 +542,16 @@ jobs:
   # `if: always()` is what makes this work: without it the job inherits the
   # default `success()` and is itself skipped the moment any dependency fails.
   #
-  # The name is an expression because `ci.yml` also fires on `labeled`, and on
-  # that event POLICY deliberately skips the PR tier (it already ran at this
-  # commit). A label run's verdict therefore says nothing about the commit's
-  # applicable suites, yet GitHub keeps only the most recent check run per name
-  # per commit, so publishing it as `Required Checks` would let a `dependencies`
-  # label turn a still-running or red commit run green (issue #5007). Label
-  # runs publish under a name nothing requires instead. Skipping the job here
-  # would not help: a skipped check run still carries the name and still counts
-  # as passing. dev/ci/check-ci-config.py enforces both halves of this.
+  # The name is an expression because ci_label.yml runs this file on `labeled`
+  # too, and on that event POLICY deliberately skips the PR tier (it already
+  # ran at this commit). A label run's verdict therefore says nothing about the
+  # commit's applicable suites, so publishing it as `Required Checks` could let
+  # a `dependencies` label turn a still-running or red commit run green (issue
+  # #5007). Label runs publish under a name nothing requires instead. Skipping
+  # the job here would not help: a skipped check run still carries the name and
+  # still counts as passing. Running label runs as a separate workflow (issue
+  # #6159) is the other half: it stops a label run from hiding this job's
+  # verdict from the merge box. dev/ci/check-ci-config.py enforces all of it.
   # ---------------------------------------------------------------------------
   required_checks:
     name: ${{ github.event.action == 'labeled' && 'Required Checks (label run)' || 'Required Checks' }}
diff --git a/.github/workflows/ci_label.yml b/.github/workflows/ci_label.yml
new file mode 100644
index 00000000000..6af3e919284
--- /dev/null
+++ b/.github/workflows/ci_label.yml
@@ -0,0 +1,56 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+# Label runs: applying a `run-*` label to a pull request runs the suite that
+# label gates at the current commit, without a new push. The pipeline is
+# ci.yml itself; POLICY in dev/ci/compute-changes.py reads the `labeled`
+# action from the event context, which a called workflow shares with its
+# caller, and runs only what the new label gates.
+#
+# This is a separate workflow, and not a `labeled` type on ci.yml's own
+# `pull_request` trigger, because of how GitHub treats two runs of one
+# workflow at the same commit: it evaluates the pull request's required checks
+# against only one of them. A pull request opened with a label already
+# applied fires `opened` and `labeled` together, and when the label run was
+# the one picked, `Required Checks` showed as "Expected" forever and the merge
+# queue never accepted the pull request (issue #6159). Runs of this workflow
+# get their own check suite, so they cannot hide the commit run's verdict.
+# Nothing here publishes a required name either: every check is nested under
+# the calling job's name, and the aggregator reports as
+# `Required Checks (label run)`.
+name: Comet CI (label run)
+
+# No `concurrency` here. ci.yml declares its own group, keyed on this
+# workflow's name and the label, and the same group on the caller as well
+# would deadlock the two against each other.
+on:
+  pull_request:
+    types: [labeled]
+
+jobs:
+  ci:
+    name: Label run
+    # A called workflow's jobs can hold no more than the caller grants, and
+    # GitHub checks that for every job when the run starts, including the
+    # ones this event skips. This is the union of what ci.yml's jobs request:
+    # `changes` and `nightly_report` read the Actions API, and
+    # `nightly_report` files issues (it only runs on the schedule).
+    permissions:
+      actions: read
+      contents: read
+      issues: write
+    uses: ./.github/workflows/ci.yml
diff --git a/dev/ci/check-ci-config.py b/dev/ci/check-ci-config.py
index 55edd5f5e27..31b69675b7a 100644
--- a/dev/ci/check-ci-config.py
+++ b/dev/ci/check-ci-config.py
@@ -34,9 +34,12 @@
 #      rename on either side of the ci.yml/.asf.yaml pair turns the required
 #      context into one that never reports, which blocks *every* merge to main
 #      until INFRA removes it by hand. The job's name must also route `labeled`
-#      runs, which skip the PR tier by design, to a name nothing requires:
-#      GitHub keeps the most recent check run per name per commit, so a label
-#      run publishing the required name would overwrite the real verdict.
+#      runs, which skip the PR tier by design, to a name nothing requires, so
+#      a label run cannot stand in for the real verdict. And `labeled` runs
+#      must come from a separate workflow (ci_label.yml) rather than ci.yml's
+#      own trigger: with two ci.yml runs at one commit, GitHub evaluates the
+#      required checks against only one of them, and when that is the label
+#      run the required context never reports (issue #6159).
 #
 #   4. Artifact-name uniqueness. Artifact names are scoped to the *run*, not
 #      to the calling workflow, and ci.yml calls the Spark SQL and Iceberg
@@ -943,6 +946,77 @@ def check_required_checks():
     return not failures
 
 
+def ci_triggers():
+    """Return {event: its `types:` list, or None} from ci.yml's top-level `on:`."""
+    lines = (WORKFLOWS / "ci.yml").read_text(encoding="utf-8").splitlines()
+    event_key = re.compile(r"^  ([a-z_]+):\s*$")
+    types_key = re.compile(r"^    types:\s*\[(.*)\]\s*$")
+    triggers = {}
+    in_on = False
+    current = None
+    for line in lines:
+        if line.startswith("on:"):
+            in_on = True
+            continue
+        if not in_on:
+            continue
+        if line and not line.startswith((" ", "#")):
+            break
+        match = event_key.match(line)
+        if match:
+            current = match.group(1)
+            triggers[current] = None
+            continue
+        match = types_key.match(line)
+        if match and current:
+            triggers[current] = [t.strip() for t in match.group(1).split(",")]
+    return triggers
+
+
+def check_label_runs_separate():
+    """`labeled` runs come from ci_label.yml, never from ci.yml's own trigger.
+
+    When one workflow runs twice at the same commit, GitHub evaluates the pull
+    request's required checks against only one of the two runs. A pull request
+    opened with a label already applied fires `opened` and `labeled` together;
+    if ci.yml took both, the label run could be the one GitHub picked, and it
+    publishes `Required Checks (label run)`, so `Required Checks` showed as
+    "Expected" forever and the merge queue never took the pull request (issue
+    #6159). A separate calling workflow gets its own check suite.
+    """
+    failures = []
+    triggers = ci_triggers()
+    pull_request_types = triggers.get("pull_request") or []
+    if "labeled" in pull_request_types:
+        failures.append(
+            "ci.yml triggers on `pull_request: labeled`. Two ci.yml runs at one "
+            "commit let the label run hide `Required Checks` from the merge box; "
+            "leave `labeled` to ci_label.yml"
+        )
+    if "workflow_call" not in triggers:
+        failures.append(
+            "ci.yml has no `workflow_call` trigger, so ci_label.yml cannot call it "
+            "and applying a `run-*` label no longer runs anything"
+        )
+
+    label_workflow = WORKFLOWS / "ci_label.yml"
+    if not label_workflow.exists():
+        failures.append(f"{label_workflow} is missing; nothing runs on `labeled`")
+    else:
+        body = label_workflow.read_text(encoding="utf-8")
+        if not re.search(r"^\s+uses:\s*\./\.github/workflows/ci\.yml\s*$", body, re.M):
+            failures.append(f"{label_workflow} does not call ./.github/workflows/ci.yml")
+        if not re.search(r"^\s+types:\s*\[\s*labeled\s*\]\s*$", body, re.M):
+            failures.append(
+                f"{label_workflow} must trigger on `pull_request: types: [labeled]` "
+                f"and nothing else; any other type would run ci.yml twice per push"
+            )
+
+    for failure in failures:
+        print(f"label runs: {failure}")
+    return not failures
+
+
 def check_cache_refresh_scope():
     """Every job in pr_build_linux.yml is either a cache writer or guarded.
 
@@ -1208,6 +1282,7 @@ def check_cache_save_scope():
     ok = check_artifact_names() and ok
     ok = check_local_actions_have_checkout() and ok
     ok = check_required_checks() and ok
+    ok = check_label_runs_separate() and ok
     ok = check_cache_refresh_scope() and ok
     ok = check_nightly_scope() and ok
     ok = check_nightly_base_fallback() and ok
diff --git a/docs/source/contributor-guide/ci.md b/docs/source/contributor-guide/ci.md
index cea032370e9..fa367de798a 100644
--- a/docs/source/contributor-guide/ci.md
+++ b/docs/source/contributor-guide/ci.md
@@ -135,9 +135,10 @@ gh pr edit <number> --add-label run-spark-3.5-tests
 ```
 
 Applying a label starts a new run immediately at the pull request's current commit. That run
-executes only the suite the label gates; the PR tier already ran at that commit and is not
-repeated. Its aggregate verdict is published as `Required Checks (label run)` rather than
-`Required Checks`, so it can be read alongside the commit run without replacing it.
+belongs to the separate `Comet CI (label run)` workflow and executes only the suite the label
+gates; the PR tier already ran at that commit and is not repeated. Its aggregate verdict is
+published as `Label run / Required Checks (label run)` rather than `Required Checks`, so it can be
+read alongside the commit run without replacing it.
 
 For a queue-tier suite, that separate name costs nothing: the merge queue runs the suite again
 before the change lands, so a failure a label run surfaced still blocks the merge later. A