diff --git a/apps/server/src/orchestration-v2/Adapters/ClaudeAdapterV2.test.ts b/apps/server/src/orchestration-v2/Adapters/ClaudeAdapterV2.test.ts
index cfd6c526b2726..01f5c9396f732 100644
--- a/apps/server/src/orchestration-v2/Adapters/ClaudeAdapterV2.test.ts
+++ b/apps/server/src/orchestration-v2/Adapters/ClaudeAdapterV2.test.ts
@@ -395,6 +395,23 @@ describe("ClaudeAdapterV2 runtime query policy", () => {
     });
   });
 
+  it("makes Auto-compact after beat CLAUDE_CODE_AUTO_COMPACT_WINDOW from settings env", () => {
+    const options = ClaudeAdapterV2.makeClaudeQueryOptions({
+      modelSelection: CLAUDE_TEST_MODEL_SELECTION,
+      nativeThreadId: "native-auto-compact-env",
+      resume: false,
+      cwd: "/workspace",
+      settings: AUTO_COMPACT_CLAUDE_SETTINGS,
+      sdkSettings: { env: { CLAUDE_CODE_AUTO_COMPACT_WINDOW: "1000000", OTHER: "kept" } },
+    });
+    const settings = options.settings as {
+      autoCompactWindow?: number;
+      env?: Record<string, string>;
+    };
+    assert.equal(settings.autoCompactWindow, 300_000);
+    assert.deepEqual(settings.env, { CLAUDE_CODE_AUTO_COMPACT_WINDOW: "300000", OTHER: "kept" });
+  });
+
   it("sends a custom model named like a Claude Code alias to the API unchanged", () => {
     const options = ClaudeAdapterV2.makeClaudeQueryOptions({
       modelSelection: { instanceId: CLAUDE_TEST_MODEL_SELECTION.instanceId, model: "opus" },
diff --git a/apps/server/src/orchestration-v2/Adapters/ClaudeAdapterV2.ts b/apps/server/src/orchestration-v2/Adapters/ClaudeAdapterV2.ts
index a58f91124f16d..814baac2d499c 100644
--- a/apps/server/src/orchestration-v2/Adapters/ClaudeAdapterV2.ts
+++ b/apps/server/src/orchestration-v2/Adapters/ClaudeAdapterV2.ts
@@ -2009,12 +2009,16 @@ export function makeClaudeQueryOptions(input: {
       : typeof input.sdkSettings === "object" && input.sdkSettings !== null
         ? ({ ...input.sdkSettings, ...selectionSettings } as ClaudeSdkSettings)
         : selectionSettings;
-  const compactQuerySettings =
+  const autoCompactWindow =
     input.settings?.autoCompactWindow === undefined || input.settings.autoCompactWindow.length === 0
+      ? undefined
+      : input.settings.autoCompactWindow;
+  const compactQuerySettings =
+    autoCompactWindow === undefined
       ? querySettings
       : ({
           ...(typeof querySettings === "object" && querySettings !== null ? querySettings : {}),
-          autoCompactWindow: Number(input.settings.autoCompactWindow),
+          autoCompactWindow: Number(autoCompactWindow),
         } as ClaudeSdkSettings);
   // Claude Code expands a bare alias to its own model, so a custom model with an alias's name
   // pins the alias to itself.
@@ -2024,9 +2028,17 @@ export function makeClaudeQueryOptions(input: {
           compiledSelection.apiModelId,
       }
     : undefined;
+  // Claude Code prefers CLAUDE_CODE_AUTO_COMPACT_WINDOW from any settings env over
+  // autoCompactWindow, and flag settings env beats the settings files.
+  const autoCompactEnv =
+    autoCompactWindow === undefined
+      ? undefined
+      : { CLAUDE_CODE_AUTO_COMPACT_WINDOW: autoCompactWindow };
   // A settings file path cannot take extra keys, so it goes through unchanged.
   const effectiveQuerySettings =
-    (input.toolSearchOverride === undefined && aliasOverrideEnv === undefined) ||
+    (input.toolSearchOverride === undefined &&
+      aliasOverrideEnv === undefined &&
+      autoCompactEnv === undefined) ||
     typeof compactQuerySettings === "string"
       ? compactQuerySettings
       : ({
@@ -2034,6 +2046,7 @@ export function makeClaudeQueryOptions(input: {
           env: {
             ...compactQuerySettings?.env,
             ...aliasOverrideEnv,
+            ...autoCompactEnv,
             ...(input.toolSearchOverride === undefined
               ? {}
               : { ENABLE_TOOL_SEARCH: input.toolSearchOverride }),