diff --git a/packages/coding-agent/src/core/model-registry.ts b/packages/coding-agent/src/core/model-registry.ts
index 362d8df5..7153d214 100644
--- a/packages/coding-agent/src/core/model-registry.ts
+++ b/packages/coding-agent/src/core/model-registry.ts
@@ -758,7 +758,7 @@ export class ModelRegistry {
 	registerProvider(providerName: string, config: ProviderConfigInput): void {
 		this.validateProviderConfig(providerName, config);
 		this.applyProviderConfig(providerName, config);
-		this.registeredProviders.set(providerName, config);
+		this.upsertRegisteredProvider(providerName, config);
 	}
 
 	/**
@@ -776,6 +776,25 @@ export class ModelRegistry {
 		this.refresh();
 	}
 
+	/**
+	 * Upsert a provider config into registeredProviders.
+	 * If the provider is already registered, defined values in the incoming config
+	 * override existing ones; undefined values are preserved from the stored config.
+	 * If the provider is not registered, the incoming config is stored as-is.
+	 */
+	private upsertRegisteredProvider(providerName: string, config: ProviderConfigInput): void {
+		const existing = this.registeredProviders.get(providerName);
+		if (!existing) {
+			this.registeredProviders.set(providerName, config);
+			return;
+		}
+		for (const k of Object.keys(config) as (keyof ProviderConfigInput)[]) {
+			if (config[k] !== undefined) {
+				(existing as Record<string, unknown>)[k] = config[k];
+			}
+		}
+	}
+
 	private validateProviderConfig(providerName: string, config: ProviderConfigInput): void {
 		if (config.streamSimple && !config.api) {
 			throw new Error(`Provider ${providerName}: "api" is required when registering streamSimple.`);
diff --git a/packages/coding-agent/test/model-registry.test.ts b/packages/coding-agent/test/model-registry.test.ts
index 9c2a6ec7..5a1260a6 100644
--- a/packages/coding-agent/test/model-registry.test.ts
+++ b/packages/coding-agent/test/model-registry.test.ts
@@ -6,7 +6,7 @@ import { getApiProvider } from "@mariozechner/pi-ai";
 import { getOAuthProvider } from "@mariozechner/pi-ai/oauth";
 import { afterEach, beforeEach, describe, expect, test } from "vitest";
 import { AuthStorage } from "../src/core/auth-storage.js";
-import { clearApiKeyCache, ModelRegistry } from "../src/core/model-registry.js";
+import { clearApiKeyCache, ModelRegistry, type ProviderConfigInput } from "../src/core/model-registry.js";
 
 describe("ModelRegistry", () => {
 	let tempDir: string;
@@ -32,11 +32,11 @@ describe("ModelRegistry", () => {
 		baseUrl: string,
 		models: Array<{ id: string; name?: string }>,
 		api: string = "anthropic-messages",
-	) {
+	): ProviderConfigInput {
 		return {
 			baseUrl,
 			apiKey: "TEST_KEY",
-			api,
+			api: api as Api,
 			models: models.map((m) => ({
 				id: m.id,
 				name: m.name ?? m.id,
@@ -952,6 +952,101 @@ describe("ModelRegistry", () => {
 			}
 			expect(threwCustomOverrideAfterUnregister).toBe(false);
 		});
+
+		describe("dynamic provider override persistence", () => {
+			test("baseUrl-only override keeps built-in provider models after refresh", () => {
+				const registry = ModelRegistry.create(authStorage, modelsJsonPath);
+
+				registry.registerProvider("anthropic", { baseUrl: "https://proxy.test/anthropic" });
+				registry.refresh();
+
+				const anthropicModels = getModelsForProvider(registry, "anthropic");
+				expect(anthropicModels.length).toBeGreaterThan(1);
+				expect(anthropicModels.every((m) => m.baseUrl === "https://proxy.test/anthropic")).toBe(true);
+			});
+
+			test("models-only override replaces built-in provider models after refresh", () => {
+				const registry = ModelRegistry.create(authStorage, modelsJsonPath);
+
+				registry.registerProvider("anthropic", {
+					...providerConfig("https://custom.test/anthropic", [{ id: "custom-claude" }], "anthropic-messages"),
+					baseUrl: "https://custom.test/anthropic",
+				});
+				registry.refresh();
+
+				expect(getModelsForProvider(registry, "anthropic").map((m) => m.id)).toEqual(["custom-claude"]);
+				expect(registry.find("anthropic", "custom-claude")?.baseUrl).toBe("https://custom.test/anthropic");
+			});
+
+			test("models plus baseUrl override replaces built-in provider models after refresh", () => {
+				const registry = ModelRegistry.create(authStorage, modelsJsonPath);
+
+				registry.registerProvider("anthropic", {
+					...providerConfig("https://custom.test/anthropic", [{ id: "custom-claude" }], "anthropic-messages"),
+					baseUrl: "https://custom.test/anthropic",
+				});
+				registry.registerProvider("anthropic", { baseUrl: "https://proxy.test/anthropic" });
+				registry.refresh();
+
+				expect(getModelsForProvider(registry, "anthropic").map((m) => m.id)).toEqual(["custom-claude"]);
+				expect(registry.find("anthropic", "custom-claude")?.baseUrl).toBe("https://proxy.test/anthropic");
+			});
+
+			test("models-only custom provider registration survives refresh", () => {
+				const registry = ModelRegistry.create(authStorage, modelsJsonPath);
+
+				registry.registerProvider(
+					"custom-provider",
+					providerConfig("https://custom.test/v1", [{ id: "custom-a" }, { id: "custom-b" }], "openai-completions"),
+				);
+				registry.refresh();
+
+				expect(getModelsForProvider(registry, "custom-provider").map((m) => m.id)).toEqual([
+					"custom-a",
+					"custom-b",
+				]);
+			});
+
+			test("baseUrl-only override keeps custom provider models after refresh", () => {
+				const registry = ModelRegistry.create(authStorage, modelsJsonPath);
+
+				registry.registerProvider(
+					"custom-provider",
+					providerConfig("https://custom.test/v1", [{ id: "custom-a" }, { id: "custom-b" }], "openai-completions"),
+				);
+				registry.registerProvider("custom-provider", { baseUrl: "https://proxy.test/custom" });
+				registry.refresh();
+
+				expect(getModelsForProvider(registry, "custom-provider").map((m) => m.id)).toEqual([
+					"custom-a",
+					"custom-b",
+				]);
+				expect(
+					getModelsForProvider(registry, "custom-provider").every(
+						(m) => m.baseUrl === "https://proxy.test/custom",
+					),
+				).toBe(true);
+			});
+
+			test("headers-only override keeps custom provider models after refresh", async () => {
+				const registry = ModelRegistry.create(authStorage, modelsJsonPath);
+
+				registry.registerProvider(
+					"custom-provider",
+					providerConfig("https://custom.test/v1", [{ id: "custom-a" }, { id: "custom-b" }], "openai-completions"),
+				);
+				registry.registerProvider("custom-provider", { headers: { "x-proxy": "enabled" } });
+				registry.refresh();
+
+				const models = getModelsForProvider(registry, "custom-provider");
+				expect(models.map((m) => m.id)).toEqual(["custom-a", "custom-b"]);
+				expect(models.every((m) => m.baseUrl === "https://custom.test/v1")).toBe(true);
+				expect(await registry.getApiKeyAndHeaders(models[0])).toMatchObject({
+					ok: true,
+					headers: { "x-proxy": "enabled" },
+				});
+			});
+		});
 	});
 
 	describe("API key resolution", () => {