diff --git a/src/agents/context.test.ts b/src/agents/context.test.ts
index ab2381e7555..5e762683ec8 100644
--- a/src/agents/context.test.ts
+++ b/src/agents/context.test.ts
@@ -57,6 +57,30 @@ describe("applyConfiguredContextWindows", () => {
     expect(cache.get("anthropic/claude-opus-4-6")).toBe(200_000);
   });
 
+  it("stores provider-qualified key so config overrides beat qualified discovery entries", () => {
+    // Scenario from reviewer: discovery emits provider-qualified IDs but config
+    // uses bare IDs — without the qualified key in cache, resolveContextTokensForModel
+    // would return the discovered value and bypass the explicit config override.
+    const cache = new Map<string, number>();
+    // Simulate discovery storing a qualified entry.
+    cache.set("google-gemini-cli/gemini-3.1-pro-preview", 1_048_576);
+    // Config override stored under bare key AND qualified key.
+    applyConfiguredContextWindows({
+      cache,
+      modelsConfig: {
+        providers: {
+          "google-gemini-cli": {
+            models: [{ id: "gemini-3.1-pro-preview", contextWindow: 200_000 }],
+          },
+        },
+      },
+    });
+
+    // Both bare and qualified keys must reflect the configured override.
+    expect(cache.get("gemini-3.1-pro-preview")).toBe(200_000);
+    expect(cache.get("google-gemini-cli/gemini-3.1-pro-preview")).toBe(200_000);
+  });
+
   it("adds config-only model context windows and ignores invalid entries", () => {
     const cache = new Map<string, number>();
     applyConfiguredContextWindows({
diff --git a/src/agents/context.ts b/src/agents/context.ts
index 710a33ecdfe..d05eebb85da 100644
--- a/src/agents/context.ts
+++ b/src/agents/context.ts
@@ -61,7 +61,7 @@ export function applyConfiguredContextWindows(params: {
   if (!providers || typeof providers !== "object") {
     return;
   }
-  for (const provider of Object.values(providers)) {
+  for (const [providerId, provider] of Object.entries(providers)) {
     if (!Array.isArray(provider?.models)) {
       continue;
     }
@@ -73,6 +73,12 @@ export function applyConfiguredContextWindows(params: {
         continue;
       }
       params.cache.set(modelId, contextWindow);
+      // When the model id is bare (no provider prefix), also store under the
+      // provider-qualified key so that qualified lookups in resolveContextTokensForModel
+      // respect explicit config overrides over discovered values.
+      if (!modelId.includes("/")) {
+        params.cache.set(`${providerId}/${modelId}`, contextWindow);
+      }
     }
   }
 }