diff --git a/core/config/load.ts b/core/config/load.ts
index e4c7e13c4f..97db75614f 100644
--- a/core/config/load.ts
+++ b/core/config/load.ts
@@ -822,6 +822,86 @@ async function buildConfigTsandReadConfigJs(ide: IDE, ideType: IdeType) {
   return readConfigJs();
 }
 
+async function loadConfigModule(configJsPath: string) {
+  try {
+    return await import(configJsPath);
+  } catch (e) {
+    console.log(e);
+    console.log(
+      "Could not load config.ts as absolute path, retrying as file url ...",
+    );
+    try {
+      return await import(localPathToUri(configJsPath));
+    } catch (fileUrlError) {
+      throw new Error("Could not load config.ts as file url either", {
+        cause: fileUrlError,
+      });
+    }
+  }
+}
+
+function clearConfigModuleCache(configJsPath: string) {
+  if (typeof require === "undefined") {
+    return;
+  }
+
+  try {
+    delete require.cache[require.resolve(configJsPath)];
+  } catch {
+    // Dynamic imports via file URLs may not populate require cache.
+  }
+}
+
+async function applyConfigModule<T>(
+  config: T,
+  configJsPath: string,
+): Promise<T> {
+  const module = await loadConfigModule(configJsPath);
+  clearConfigModuleCache(configJsPath);
+
+  if (!module.modifyConfig) {
+    throw new Error("config.ts does not export a modifyConfig function.");
+  }
+
+  return module.modifyConfig(config);
+}
+
+export async function applyConfigTsAndRemoteConfig<T>(options: {
+  config: T;
+  ide: IDE;
+  ideType: IdeType;
+  remoteConfigServerUrl?: string;
+}): Promise<T> {
+  const { config, ide, ideType, remoteConfigServerUrl } = options;
+
+  let modifiedConfig = config;
+
+  const configJsContents = await buildConfigTsandReadConfigJs(ide, ideType);
+  if (configJsContents) {
+    try {
+      modifiedConfig = await applyConfigModule(
+        modifiedConfig,
+        getConfigJsPath(),
+      );
+    } catch (e) {
+      console.log("Error loading config.ts: ", e);
+    }
+  }
+
+  if (remoteConfigServerUrl) {
+    try {
+      modifiedConfig = await applyConfigModule(
+        modifiedConfig,
+        getConfigJsPathForRemote(remoteConfigServerUrl),
+      );
+    } catch (e) {
+      console.log("Error loading remotely set config.js: ", e);
+    }
+  }
+
+  return modifiedConfig;
+}
+
 async function loadContinueConfigFromJson(
   ide: IDE,
   ideSettings: IdeSettings,
@@ -857,63 +937,12 @@ async function loadContinueConfigFromJson(
   // Convert serialized to intermediate config
   let intermediate = await serializedToIntermediateConfig(withShared, ide);
 
-  // Apply config.ts to modify intermediate config
-  const configJsContents = await buildConfigTsandReadConfigJs(
+  intermediate = await applyConfigTsAndRemoteConfig({
+    config: intermediate,
     ide,
-    ideInfo.ideType,
-  );
-  if (configJsContents) {
-    try {
-      // Try config.ts first
-      const configJsPath = getConfigJsPath();
-      let module: any;
-
-      try {
-        module = await import(configJsPath);
-      } catch (e) {
-        console.log(e);
-        console.log(
-          "Could not load config.ts as absolute path, retrying as file url ...",
-        );
-        try {
-          module = await import(localPathToUri(configJsPath));
-        } catch (e) {
-          throw new Error("Could not load config.ts as file url either", {
-            cause: e,
-          });
-        }
-      }
-
-      if (typeof require !== "undefined") {
-        delete require.cache[require.resolve(configJsPath)];
-      }
-      if (!module.modifyConfig) {
-        throw new Error("config.ts does not export a modifyConfig function.");
-      }
-      intermediate = module.modifyConfig(intermediate);
-    } catch (e) {
-      console.log("Error loading config.ts: ", e);
-    }
-  }
-
-  // Apply remote config.js to modify intermediate config
-  if (ideSettings.remoteConfigServerUrl) {
-    try {
-      const configJsPathForRemote = getConfigJsPathForRemote(
-        ideSettings.remoteConfigServerUrl,
-      );
-      const module = await import(configJsPathForRemote);
-      if (typeof require !== "undefined") {
-        delete require.cache[require.resolve(configJsPathForRemote)];
-      }
-      if (!module.modifyConfig) {
-        throw new Error("config.ts does not export a modifyConfig function.");
-      }
-      intermediate = module.modifyConfig(intermediate);
-    } catch (e) {
-      console.log("Error loading remotely set config.js: ", e);
-    }
-  }
+    ideType: ideInfo.ideType,
+    remoteConfigServerUrl: ideSettings.remoteConfigServerUrl,
+  });
 
   // Convert to final config format
   const { config: finalConfig, errors: finalErrors } =
diff --git a/core/config/yaml/loadContinueConfigFromYaml.vitest.ts b/core/config/yaml/loadContinueConfigFromYaml.vitest.ts
new file mode 100644
index 0000000000..6e29bb35d9
--- /dev/null
+++ b/core/config/yaml/loadContinueConfigFromYaml.vitest.ts
@@ -0,0 +1,114 @@
+import { describe, expect, it, vi } from "vitest";
+
+const { mockApplyConfigTsAndRemoteConfig } = vi.hoisted(() => ({
+  mockApplyConfigTsAndRemoteConfig: vi.fn(async ({ config }) => ({
+    ...config,
+    allowAnonymousTelemetry: false,
+  })),
+}));
+
+vi.mock("../load", () => ({
+  applyConfigTsAndRemoteConfig: mockApplyConfigTsAndRemoteConfig,
+}));
+
+vi.mock("../../context/mcp/MCPManagerSingleton", () => ({
+  MCPManagerSingleton: {
+    getInstance: () => ({
+      setConnections: vi.fn(),
+      shutdown: vi.fn(),
+      getStatuses: () => [],
+    }),
+  },
+}));
+
+vi.mock("../../promptFiles/getPromptFiles", () => ({
+  getAllPromptFiles: vi.fn().mockResolvedValue([]),
+}));
+
+vi.mock("../../context/mcp/json/loadJsonMcpConfigs", () => ({
+  loadJsonMcpConfigs: vi.fn().mockResolvedValue({ errors: [], mcpServers: [] }),
+}));
+
+vi.mock("../../tools", () => ({
+  getBaseToolDefinitions: vi.fn().mockReturnValue([]),
+}));
+
+vi.mock("../loadContextProviders", () => ({
+  loadConfigContextProviders: vi.fn().mockReturnValue({
+    providers: [],
+    errors: [],
+  }),
+}));
+
+vi.mock("../loadLocalAssistants", () => ({
+  getAllDotContinueDefinitionFiles: vi.fn().mockResolvedValue([]),
+}));
+
+vi.mock("./models", () => ({
+  llmsFromModelConfig: vi.fn().mockResolvedValue([]),
+}));
+
+vi.mock("../../util/GlobalContext", () => ({
+  GlobalContext: class {
+    getSharedConfig() {
+      return {};
+    }
+
+    get() {
+      return {};
+    }
+
+    update() {}
+  },
+}));
+
+vi.mock("../../control-plane/env", () => ({
+  getControlPlaneEnvSync: vi.fn().mockReturnValue({
+    CONTROL_PLANE_URL: "https://api.example.com",
+  }),
+}));
+
+vi.mock("../../control-plane/PolicySingleton", () => ({
+  PolicySingleton: {
+    getInstance: () => ({ policy: null }),
+  },
+}));
+
+import { loadContinueConfigFromYaml } from "./loadYaml";
+
+describe("loadContinueConfigFromYaml", () => {
+  it("applies config.ts modifiers for YAML configs", async () => {
+    const result = await loadContinueConfigFromYaml({
+      ide: {} as any,
+      ideSettings: {
+        remoteConfigServerUrl: "",
+        remoteConfigSyncPeriod: 60,
+        userToken: "",
+        continueTestEnvironment: "none",
+        pauseCodebaseIndexOnStart: false,
+      },
+      ideInfo: { ideType: "vscode" } as any,
+      uniqueId: "test-unique-id",
+      llmLogger: {} as any,
+      workOsAccessToken: undefined,
+      overrideConfigYaml: {
+        name: "Local Config",
+        version: "1.0.0",
+        schema: "v1",
+        models: [],
+      },
+      controlPlaneClient: {
+        getAccessToken: vi.fn(),
+      } as any,
+      orgScopeId: null,
+      packageIdentifier: {
+        uriType: "file",
+        fileUri: "/tmp/config.yaml",
+        content: "name: Local Config\nversion: 1.0.0\nschema: v1\n",
+      },
+    });
+
+    expect(mockApplyConfigTsAndRemoteConfig).toHaveBeenCalledTimes(1);
+    expect(result.config?.allowAnonymousTelemetry).toBe(false);
+  });
+});
diff --git a/core/config/yaml/loadYaml.ts b/core/config/yaml/loadYaml.ts
index f7a82635b6..18edc8d73b 100644
--- a/core/config/yaml/loadYaml.ts
+++ b/core/config/yaml/loadYaml.ts
@@ -27,6 +27,7 @@ import { ControlPlaneClient } from "../../control-plane/client";
 import TransformersJsEmbeddingsProvider from "../../llm/llms/TransformersJsEmbeddingsProvider";
 import { getAllPromptFiles } from "../../promptFiles/getPromptFiles";
 import { GlobalContext } from "../../util/GlobalContext";
+import { applyConfigTsAndRemoteConfig } from "../load";
 import { modifyAnyConfigWithSharedConfig } from "../sharedConfig";
 
 import { convertPromptBlockToSlashCommand } from "../../commands/slash/promptBlockSlashCommand";
@@ -492,8 +493,15 @@ export async function loadContinueConfigFromYaml(options: {
     withShared.allowAnonymousTelemetry = true;
   }
 
-  return {
+  const withConfigTs = await applyConfigTsAndRemoteConfig({
     config: withShared,
+    ide,
+    ideType: ideInfo.ideType,
+    remoteConfigServerUrl: ideSettings.remoteConfigServerUrl,
+  });
+
+  return {
+    config: withConfigTs,
     errors: [...(configYamlResult.errors ?? []), ...localErrors],
     configLoadInterrupted: false,
     configName: configYamlResult.configName,