diff --git a/scripts/upstream/queue.test.ts b/scripts/upstream/queue.test.ts
index 7301b484ea8a..59bc290ddf14 100644
--- a/scripts/upstream/queue.test.ts
+++ b/scripts/upstream/queue.test.ts
@@ -222,14 +222,19 @@ describe("chronological upstream queue", () => {
     const input = [integration(1), integration(2), integration(3)];
     const cache = { [sha(1)]: [pr], [sha(2)]: [pr], [sha(3)]: [{ ...pr, mergedAt: null }] };
     assert.deepEqual(
-      associatePRs(input, cache, "example/upstream", new Set([sha(2)])).map((entry) => entry.pr),
+      associatePRs(input, cache, "example/upstream", new Set([sha(2)]), new Set([sha(2)])).map(
+        (entry) => entry.pr,
+      ),
       [12, 12, null],
     );
     assert.throws(
-      () => associatePRs(input, cache, "example/upstream", new Set()),
+      () => associatePRs(input, cache, "example/upstream", new Set(), new Set([sha(2)])),
       "outside target",
     );
-    assert.throws(() => associatePRs(input, {}, "example/upstream", new Set()), "Missing GitHub");
+    assert.throws(
+      () => associatePRs(input, {}, "example/upstream", new Set(), new Set()),
+      "Missing GitHub",
+    );
     assert.throws(
       () =>
         associatePRs(
@@ -237,6 +242,7 @@ describe("chronological upstream queue", () => {
           { [sha(1)]: [pr, { ...pr, number: 13 }] },
           "example/upstream",
           new Set([sha(2)]),
+          new Set([sha(2)]),
         ),
       "Ambiguous",
     );
@@ -256,7 +262,13 @@ describe("chronological upstream queue", () => {
       [sha(2)]: [pr],
       [sha(3)]: [{ ...pr, baseRepository: { nameWithOwner: "example/other" } }],
     };
-    const associated = associatePRs(integrations, cache, "example/upstream", new Set([sha(2)]));
+    const associated = associatePRs(
+      integrations,
+      cache,
+      "example/upstream",
+      new Set([sha(2)]),
+      new Set([sha(2)]),
+    );
     assert.deepEqual(
       associated.map((entry) => entry.pr),
       [12, 12, null],
@@ -271,7 +283,33 @@ describe("chronological upstream queue", () => {
       [sha(3)],
     );
     assert.throws(
-      () => associatePRs(integrations, cache, "example/upstream", new Set()),
+      () => associatePRs(integrations, cache, "example/upstream", new Set(), new Set([sha(2)])),
+      "outside target",
+    );
+  });
+
+  it("treats a commit that a side branch's sync PR carried as a direct commit", () => {
+    const syncPR = {
+      number: 30,
+      mergedAt: "2026-01-02",
+      baseRefName: "feature/long-lived",
+      baseRepository: { nameWithOwner: "example/upstream" },
+      // The sync PR merged into the side branch, so its merge commit is not on main.
+      mergeCommit: { oid: sha(9) },
+    };
+    const squashPR = { ...syncPR, number: 31, baseRefName: "main", mergeCommit: { oid: sha(2) } };
+    const integrations = [integration(1), integration(2)];
+    const cache = { [sha(1)]: [syncPR], [sha(2)]: [squashPR, syncPR] };
+    const mainline = new Set([sha(1), sha(2)]);
+    assert.deepEqual(
+      associatePRs(integrations, cache, "example/upstream", mainline, mainline).map(
+        (entry) => entry.pr,
+      ),
+      [null, 31],
+    );
+    // A PR that did merge into main still may not be split by the target.
+    assert.throws(
+      () => associatePRs(integrations, cache, "example/upstream", new Set([sha(1)]), mainline),
       "outside target",
     );
   });
diff --git a/scripts/upstream/queue.ts b/scripts/upstream/queue.ts
index 82df97d3d5e7..9c110200ec5d 100644
--- a/scripts/upstream/queue.ts
+++ b/scripts/upstream/queue.ts
@@ -331,14 +331,20 @@ export function associatePRs(
   associations: Associations,
   repository: string,
   chain: Set<string>,
+  mainline: ReadonlySet<string>,
 ): Integration[] {
   return integrations.map((entry) => {
     const prs = associations[entry.sha];
     if (!prs) throw new Error(`Missing GitHub metadata for ${entry.sha}.`);
     // A PR can merge into an intermediate branch before its commits reach main.
     // The target's first-parent chain, not the PR's base branch name, establishes coverage.
+    // A PR whose merge commit never lands on upstream main's first-parent history only
+    // carried this commit into a side branch, as a "merge main into" sync PR does.
     const merged = prs.filter(
-      (pr) => pr.mergedAt !== null && pr.baseRepository.nameWithOwner === repository,
+      (pr) =>
+        pr.mergedAt !== null &&
+        pr.baseRepository.nameWithOwner === repository &&
+        (pr.mergeCommit === null || mainline.has(pr.mergeCommit.oid)),
     );
     if (merged.some((pr) => !pr.mergeCommit || !chain.has(pr.mergeCommit.oid))) {
       throw new Error(
@@ -537,6 +543,7 @@ function main() {
     associations,
     state.upstreamRepository,
     targetChain,
+    new Set(upstreamChain),
   );
   if (command === "target") {
     NodeFS.writeFileSync(statePath, `${JSON.stringify(state, null, 2)}\n`);