diff --git a/packages/coding-agent/CHANGELOG.md b/packages/coding-agent/CHANGELOG.md
index 38ab79c4b..fb692f7c4 100644
--- a/packages/coding-agent/CHANGELOG.md
+++ b/packages/coding-agent/CHANGELOG.md
@@ -25,7 +25,7 @@
 - Fixed edit streaming preview updates to cancel obsolete in-flight computations and avoid rendering stale previews as args change
 - Fixed Mermaid fenced markdown rendering in assistant messages on terminals without image protocol support ([#650](https://github.com/can1357/oh-my-pi/issues/650))
 - Fixed SQLite `read` helper queries to reject `where=` clauses with SQL control syntax that could override the structured selector's pagination; raw SQL remains available through `q=SELECT ...`
-- Fixed `models` provider transport overrides so `headers`-only entries apply without requiring `baseUrl`, including runtime `registerProvider()` overrides that now persist across `refresh()` / `refreshProvider()`, preserve existing `baseUrl` on subsequent headers-only updates, and clear stale transport overrides when a provider is re-registered under a different extension source
+- Fixed `models` provider transport overrides so `headers`-only entries apply without requiring `baseUrl`, including runtime `registerProvider()` overrides that now persist across `refresh()` / `refreshProvider()`, preserve existing `baseUrl` on subsequent headers-only updates, clear stale transport overrides when a provider is re-registered under a different extension source, and keep runtime transport headers authoritative when `modelOverrides` set overlapping header keys
 
 ## [14.2.0] - 2026-04-23
 
diff --git a/packages/coding-agent/src/config/model-registry.ts b/packages/coding-agent/src/config/model-registry.ts
index fa10f0897..b1c34e0a2 100644
--- a/packages/coding-agent/src/config/model-registry.ts
+++ b/packages/coding-agent/src/config/model-registry.ts
@@ -886,9 +886,8 @@ export class ModelRegistry {
 		const withConfigModels = this.#mergeCustomModels(resolvedDefaults, this.#customModelOverlays);
 		// Merge runtime extension models so they survive refresh() cycles
 		const combined = this.#mergeCustomModels(withConfigModels, this.#runtimeModelOverlays);
-		const withRuntimeProviderOverrides = this.#applyRuntimeProviderOverrides(combined);
-
-		this.#models = this.#applyModelOverrides(withRuntimeProviderOverrides, this.#modelOverrides);
+		const withModelOverrides = this.#applyModelOverrides(combined, this.#modelOverrides);
+		this.#models = this.#applyRuntimeProviderOverrides(withModelOverrides);
 		this.#rebuildCanonicalIndex();
 	}
 
@@ -1179,8 +1178,8 @@ export class ModelRegistry {
 		const withConfigModels = this.#mergeCustomModels(resolved, this.#customModelOverlays);
 		// Merge runtime extension models so they survive online discovery completion
 		const combined = this.#mergeCustomModels(withConfigModels, this.#runtimeModelOverlays);
-		const withRuntimeProviderOverrides = this.#applyRuntimeProviderOverrides(combined);
-		this.#models = this.#applyModelOverrides(withRuntimeProviderOverrides, this.#modelOverrides);
+		const withModelOverrides = this.#applyModelOverrides(combined, this.#modelOverrides);
+		this.#models = this.#applyRuntimeProviderOverrides(withModelOverrides);
 		this.#rebuildCanonicalIndex();
 	}
 
diff --git a/packages/coding-agent/test/model-registry-runtime-provider.test.ts b/packages/coding-agent/test/model-registry-runtime-provider.test.ts
index c6e3f684c..80e059be2 100644
--- a/packages/coding-agent/test/model-registry-runtime-provider.test.ts
+++ b/packages/coding-agent/test/model-registry-runtime-provider.test.ts
@@ -295,6 +295,49 @@ describe("ModelRegistry runtime provider registration", () => {
 		expect(registry.find("runtime-provider", modelId)).toBeUndefined();
 	});
 
+	test("runtime headers override modelOverrides headers across refresh cycles", async () => {
+		const initialRegistry = new ModelRegistry(authStorage, modelsJsonPath);
+		const targetModel = initialRegistry.getAll().find(model => model.provider === "anthropic");
+		if (!targetModel) throw new Error("Expected bundled anthropic model");
+
+		const modelId = targetModel.id;
+		const sharedHeader = "X-Shared-Provider-Model-Header";
+		const configHeaderValue = "config-header";
+		const runtimeHeaderValue = "runtime-header";
+
+		fs.writeFileSync(
+			modelsJsonPath,
+			JSON.stringify({
+				providers: {
+					anthropic: {
+						modelOverrides: {
+							[modelId]: { headers: { [sharedHeader]: configHeaderValue } },
+						},
+					},
+				},
+			}),
+		);
+
+		const registry = new ModelRegistry(authStorage, modelsJsonPath);
+		expect(registry.find("anthropic", modelId)?.headers?.[sharedHeader]).toBe(configHeaderValue);
+
+		registry.registerProvider(
+			"anthropic",
+			{ headers: { [sharedHeader]: runtimeHeaderValue } },
+			"ext://runtime",
+		);
+		expect(registry.find("anthropic", modelId)?.headers?.[sharedHeader]).toBe(runtimeHeaderValue);
+
+		await registry.refresh("offline");
+		expect(registry.find("anthropic", modelId)?.headers?.[sharedHeader]).toBe(runtimeHeaderValue);
+
+		await registry.refreshProvider("anthropic", "offline");
+		expect(registry.find("anthropic", modelId)?.headers?.[sharedHeader]).toBe(runtimeHeaderValue);
+
+		registry.clearSourceRegistrations("ext://runtime");
+		expect(registry.find("anthropic", modelId)?.headers?.[sharedHeader]).toBe(configHeaderValue);
+	});
+
 	test("extension-registered API keys survive refresh cycle for auth resolution", async () => {
 		const registry = new ModelRegistry(authStorage, modelsJsonPath);