diff --git a/extensions/ql-vscode/src/common/app.ts b/extensions/ql-vscode/src/common/app.ts
index 278ea2b9d..2e749c018 100644
--- a/extensions/ql-vscode/src/common/app.ts
+++ b/extensions/ql-vscode/src/common/app.ts
@@ -7,7 +7,6 @@ import { AppCommandManager } from "./commands";
 
 export interface App {
   createEventEmitter<T>(): AppEventEmitter<T>;
-  executeCommand(command: string, ...args: any): Thenable<void>;
   readonly mode: AppMode;
   readonly logger: Logger;
   readonly subscriptions: Disposable[];
diff --git a/extensions/ql-vscode/src/common/commands.ts b/extensions/ql-vscode/src/common/commands.ts
index a41a57b8f..aa7792624 100644
--- a/extensions/ql-vscode/src/common/commands.ts
+++ b/extensions/ql-vscode/src/common/commands.ts
@@ -36,6 +36,10 @@ export type SingleSelectionCommandFunction<Item> = (
 // See https://code.visualstudio.com/api/references/commands
 export type BuiltInVsCodeCommands = {
   "markdown.showPreviewToSide": (uri: Uri) => Promise<void>;
+  setContext: (
+    key: `${"codeql" | "codeQL"}${string}`,
+    value: unknown,
+  ) => Promise<void>;
   "workbench.action.reloadWindow": () => Promise<void>;
 };
 
diff --git a/extensions/ql-vscode/src/common/vscode/vscode-app.ts b/extensions/ql-vscode/src/common/vscode/vscode-app.ts
index 54032a8b1..a8f9da973 100644
--- a/extensions/ql-vscode/src/common/vscode/vscode-app.ts
+++ b/extensions/ql-vscode/src/common/vscode/vscode-app.ts
@@ -61,8 +61,4 @@ export class ExtensionApp implements App {
   public createEventEmitter<T>(): AppEventEmitter<T> {
     return new VSCodeAppEventEmitter<T>();
   }
-
-  public executeCommand(command: string, ...args: any): Thenable<void> {
-    return vscode.commands.executeCommand(command, ...args);
-  }
 }
diff --git a/extensions/ql-vscode/src/databases/config/db-config-store.ts b/extensions/ql-vscode/src/databases/config/db-config-store.ts
index 54a3c549d..3013d164f 100644
--- a/extensions/ql-vscode/src/databases/config/db-config-store.ts
+++ b/extensions/ql-vscode/src/databases/config/db-config-store.ts
@@ -391,14 +391,14 @@ export class DbConfigStore extends DisposableObject {
 
     if (this.configErrors.length === 0) {
       this.config = newConfig;
-      await this.app.executeCommand(
+      await this.app.commands.execute(
         "setContext",
         "codeQLVariantAnalysisRepositories.configError",
         false,
       );
     } else {
       this.config = undefined;
-      await this.app.executeCommand(
+      await this.app.commands.execute(
         "setContext",
         "codeQLVariantAnalysisRepositories.configError",
         true,
@@ -426,14 +426,14 @@ export class DbConfigStore extends DisposableObject {
 
     if (this.configErrors.length === 0) {
       this.config = newConfig;
-      void this.app.executeCommand(
+      void this.app.commands.execute(
         "setContext",
         "codeQLVariantAnalysisRepositories.configError",
         false,
       );
     } else {
       this.config = undefined;
-      void this.app.executeCommand(
+      void this.app.commands.execute(
         "setContext",
         "codeQLVariantAnalysisRepositories.configError",
         true,
diff --git a/extensions/ql-vscode/test/__mocks__/appMock.ts b/extensions/ql-vscode/test/__mocks__/appMock.ts
index 6a4b05ba8..1b6d9da9d 100644
--- a/extensions/ql-vscode/test/__mocks__/appMock.ts
+++ b/extensions/ql-vscode/test/__mocks__/appMock.ts
@@ -14,7 +14,6 @@ export function createMockApp({
   workspaceStoragePath = "/mock/workspace/storage/path",
   globalStoragePath = "/mock/global/storage/path",
   createEventEmitter = <T>() => new MockAppEventEmitter<T>(),
-  executeCommand = jest.fn(() => Promise.resolve()),
   workspaceState = createMockMemento(),
   credentials = testCredentialsWithStub(),
   commands = createMockCommandManager(),
@@ -23,7 +22,6 @@ export function createMockApp({
   workspaceStoragePath?: string;
   globalStoragePath?: string;
   createEventEmitter?: <T>() => AppEventEmitter<T>;
-  executeCommand?: () => Promise<void>;
   workspaceState?: Memento;
   credentials?: Credentials;
   commands?: AppCommandManager;
@@ -37,7 +35,6 @@ export function createMockApp({
     globalStoragePath,
     workspaceState,
     createEventEmitter,
-    executeCommand,
     credentials,
     commands,
   };
diff --git a/extensions/ql-vscode/test/unit-tests/databases/config/db-config-store.test.ts b/extensions/ql-vscode/test/unit-tests/databases/config/db-config-store.test.ts
index 7e0af0d86..ca4b7ead6 100644
--- a/extensions/ql-vscode/test/unit-tests/databases/config/db-config-store.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/databases/config/db-config-store.test.ts
@@ -19,6 +19,7 @@ import {
   createRemoteUserDefinedListDbItem,
 } from "../../../factories/db-item-factories";
 import { createMockApp } from "../../../__mocks__/appMock";
+import { createMockCommandManager } from "../../../__mocks__/commandsMock";
 
 describe("db config store", () => {
   const extensionPath = join(__dirname, "../../../..");
@@ -136,14 +137,16 @@ describe("db config store", () => {
     it("should set codeQLVariantAnalysisRepositories.configError to true when config has error", async () => {
       const testDataStoragePathInvalid = join(__dirname, "data", "invalid");
 
+      const executeCommand = jest.fn();
       const app = createMockApp({
         extensionPath,
         workspaceStoragePath: testDataStoragePathInvalid,
+        commands: createMockCommandManager({ executeCommand }),
       });
       const configStore = new DbConfigStore(app, false);
       await configStore.initialize();
 
-      expect(app.executeCommand).toBeCalledWith(
+      expect(executeCommand).toBeCalledWith(
         "setContext",
         "codeQLVariantAnalysisRepositories.configError",
         true,
@@ -152,14 +155,16 @@ describe("db config store", () => {
     });
 
     it("should set codeQLVariantAnalysisRepositories.configError to false when config is valid", async () => {
+      const executeCommand = jest.fn();
       const app = createMockApp({
         extensionPath,
         workspaceStoragePath: testDataStoragePath,
+        commands: createMockCommandManager({ executeCommand }),
       });
       const configStore = new DbConfigStore(app, false);
       await configStore.initialize();
 
-      expect(app.executeCommand).toBeCalledWith(
+      expect(executeCommand).toBeCalledWith(
         "setContext",
         "codeQLVariantAnalysisRepositories.configError",
         false,