diff --git a/extensions/ql-vscode/src/extension.ts b/extensions/ql-vscode/src/extension.ts
index 8be2d5078..edfdd080c 100644
--- a/extensions/ql-vscode/src/extension.ts
+++ b/extensions/ql-vscode/src/extension.ts
@@ -790,7 +790,7 @@ async function activateWithInstalledDistribution(
   );
   ctx.subscriptions.push(databaseUI);
 
-  QueriesModule.initialize(app, cliServer);
+  QueriesModule.initialize(app, languageContext, cliServer);
 
   void extLogger.log("Initializing evaluator log viewer.");
   const evalLogViewer = new EvalLogViewer();
diff --git a/extensions/ql-vscode/src/queries-panel/queries-module.ts b/extensions/ql-vscode/src/queries-panel/queries-module.ts
index 69d70eba7..efb6d1e93 100644
--- a/extensions/ql-vscode/src/queries-panel/queries-module.ts
+++ b/extensions/ql-vscode/src/queries-panel/queries-module.ts
@@ -6,6 +6,7 @@ import { DisposableObject } from "../common/disposable-object";
 import { QueriesPanel } from "./queries-panel";
 import { QueryDiscovery } from "./query-discovery";
 import { QueryPackDiscovery } from "./query-pack-discovery";
+import { LanguageContextStore } from "../language-context-store";
 
 export class QueriesModule extends DisposableObject {
   private queriesPanel: QueriesPanel | undefined;
@@ -16,16 +17,21 @@ export class QueriesModule extends DisposableObject {
 
   public static initialize(
     app: App,
+    languageContext: LanguageContextStore,
     cliServer: CodeQLCliServer,
   ): QueriesModule {
     const queriesModule = new QueriesModule(app);
     app.subscriptions.push(queriesModule);
 
-    queriesModule.initialize(app, cliServer);
+    queriesModule.initialize(app, languageContext, cliServer);
     return queriesModule;
   }
 
-  private initialize(app: App, cliServer: CodeQLCliServer): void {
+  private initialize(
+    app: App,
+    langauageContext: LanguageContextStore,
+    cliServer: CodeQLCliServer,
+  ): void {
     // Currently, we only want to expose the new panel when we are in canary mode
     // and the user has enabled the "Show queries panel" flag.
     if (!isCanary() || !showQueriesPanel()) {
@@ -38,8 +44,9 @@ export class QueriesModule extends DisposableObject {
     void queryPackDiscovery.initialRefresh();
 
     const queryDiscovery = new QueryDiscovery(
-      app.environment,
+      app,
       queryPackDiscovery,
+      langauageContext,
     );
     this.push(queryDiscovery);
     void queryDiscovery.initialRefresh();
diff --git a/extensions/ql-vscode/src/queries-panel/query-discovery.ts b/extensions/ql-vscode/src/queries-panel/query-discovery.ts
index 83db85532..0649dba73 100644
--- a/extensions/ql-vscode/src/queries-panel/query-discovery.ts
+++ b/extensions/ql-vscode/src/queries-panel/query-discovery.ts
@@ -1,6 +1,6 @@
 import { dirname, basename, normalize, relative } from "path";
 import { Event } from "vscode";
-import { EnvironmentContext } from "../common/app";
+import { App } from "../common/app";
 import {
   FileTreeDirectory,
   FileTreeLeaf,
@@ -11,6 +11,8 @@ import { FilePathDiscovery } from "../common/vscode/file-path-discovery";
 import { containsPath } from "../common/files";
 import { getOnDiskWorkspaceFoldersObjects } from "../common/vscode/workspace-folders";
 import { QueryLanguage } from "../common/query-language";
+import { LanguageContextStore } from "../language-context-store";
+import { AppEvent, AppEventEmitter } from "../common/events";
 
 const QUERY_FILE_EXTENSION = ".ql";
 
@@ -31,24 +33,36 @@ export class QueryDiscovery
   extends FilePathDiscovery<Query>
   implements QueryDiscoverer
 {
+  public readonly onDidChangeQueries: AppEvent<void>;
+  private readonly onDidChangeQueriesEmitter: AppEventEmitter<void>;
+
   constructor(
-    private readonly env: EnvironmentContext,
+    private readonly app: App,
     private readonly queryPackDiscovery: QueryPackDiscoverer,
+    private readonly languageContext: LanguageContextStore,
   ) {
     super("Query Discovery", `**/*${QUERY_FILE_EXTENSION}`);
 
+    // Set up event emitters
+    this.onDidChangeQueriesEmitter = this.push(app.createEventEmitter<void>());
+    this.onDidChangeQueries = this.onDidChangeQueriesEmitter.event;
+
+    // Handlers
     this.push(
       this.queryPackDiscovery.onDidChangeQueryPacks(
         this.recomputeAllData.bind(this),
       ),
     );
-  }
-
-  /**
-   * Event that fires when the set of queries in the workspace changes.
-   */
-  public get onDidChangeQueries(): Event<void> {
-    return this.onDidChangePathData;
+    this.push(
+      this.onDidChangePathData(() => {
+        this.onDidChangeQueriesEmitter.fire();
+      }),
+    );
+    this.push(
+      this.languageContext.onLanguageContextChanged(() => {
+        this.onDidChangeQueriesEmitter.fire();
+      }),
+    );
   }
 
   /**
@@ -64,8 +78,10 @@ export class QueryDiscovery
 
     const roots = [];
     for (const workspaceFolder of getOnDiskWorkspaceFoldersObjects()) {
-      const queriesInRoot = pathData.filter((query) =>
-        containsPath(workspaceFolder.uri.fsPath, query.path),
+      const queriesInRoot = pathData.filter(
+        (query) =>
+          containsPath(workspaceFolder.uri.fsPath, query.path) &&
+          this.languageContext.shouldInclude(query.language),
       );
       if (queriesInRoot.length === 0) {
         continue;
@@ -73,7 +89,7 @@ export class QueryDiscovery
       const root = new FileTreeDirectory<string>(
         workspaceFolder.uri.fsPath,
         workspaceFolder.name,
-        this.env,
+        this.app.environment,
       );
       for (const query of queriesInRoot) {
         const dirName = dirname(normalize(relative(root.path, query.path)));
diff --git a/extensions/ql-vscode/test/__mocks__/appMock.ts b/extensions/ql-vscode/test/__mocks__/appMock.ts
index 0a596ef33..797ea3d13 100644
--- a/extensions/ql-vscode/test/__mocks__/appMock.ts
+++ b/extensions/ql-vscode/test/__mocks__/appMock.ts
@@ -56,7 +56,7 @@ class MockAppEventEmitter<T> implements AppEventEmitter<T> {
 
   constructor() {
     this.event = () => {
-      return {} as Disposable;
+      return new MockAppEvent();
     };
   }
 
@@ -69,7 +69,17 @@ class MockAppEventEmitter<T> implements AppEventEmitter<T> {
   }
 }
 
-export function createMockEnvironmentContext(): EnvironmentContext {
+class MockAppEvent implements Disposable {
+  public fire(): void {
+    // no-op
+  }
+
+  public dispose() {
+    // no-op
+  }
+}
+
+function createMockEnvironmentContext(): EnvironmentContext {
   return {
     language: "en-US",
   };
diff --git a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/queries-panel/query-discovery.test.ts b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/queries-panel/query-discovery.test.ts
index 24fd95a42..fc4dc57b4 100644
--- a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/queries-panel/query-discovery.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/queries-panel/query-discovery.test.ts
@@ -3,8 +3,8 @@ import {
   QueryDiscovery,
   QueryPackDiscoverer,
 } from "../../../../src/queries-panel/query-discovery";
-import { createMockEnvironmentContext } from "../../../__mocks__/appMock";
-import { dirname, join } from "path";
+import { createMockApp } from "../../../__mocks__/appMock";
+import { basename, dirname, join } from "path";
 import * as tmp from "tmp";
 import {
   FileTreeDirectory,
@@ -13,6 +13,7 @@ import {
 import { mkdirSync, writeFileSync } from "fs";
 import { QueryLanguage } from "../../../../src/common/query-language";
 import { sleep } from "../../../../src/common/time";
+import { LanguageContextStore } from "../../../../src/language-context-store";
 
 describe("Query pack discovery", () => {
   let tmpDir: string;
@@ -20,7 +21,10 @@ describe("Query pack discovery", () => {
 
   let workspacePath: string;
 
-  const env = createMockEnvironmentContext();
+  const app = createMockApp({});
+  const env = app.environment;
+
+  const languageContext = new LanguageContextStore(app);
 
   const onDidChangeQueryPacks = new EventEmitter<void>();
   let queryPackDiscoverer: QueryPackDiscoverer;
@@ -45,7 +49,7 @@ describe("Query pack discovery", () => {
       getLanguageForQueryFile: () => QueryLanguage.Java,
       onDidChangeQueryPacks: onDidChangeQueryPacks.event,
     };
-    discovery = new QueryDiscovery(env, queryPackDiscoverer);
+    discovery = new QueryDiscovery(app, queryPackDiscoverer, languageContext);
   });
 
   afterEach(() => {
@@ -160,6 +164,52 @@ describe("Query pack discovery", () => {
         ]),
       ]);
     });
+
+    it("should respect the language context filter", async () => {
+      makeTestFile(join(workspacePath, "query1.ql"));
+      makeTestFile(join(workspacePath, "query2.ql"));
+
+      queryPackDiscoverer.getLanguageForQueryFile = (path) => {
+        if (basename(path) === "query1.ql") {
+          return QueryLanguage.Java;
+        } else {
+          return QueryLanguage.Python;
+        }
+      };
+
+      await discovery.initialRefresh();
+
+      // Set the language to python-only
+      await languageContext.setLanguageContext(QueryLanguage.Python);
+
+      expect(discovery.buildQueryTree()).toEqual([
+        new FileTreeDirectory(workspacePath, "workspace", env, [
+          new FileTreeLeaf(
+            join(workspacePath, "query2.ql"),
+            "query2.ql",
+            "python",
+          ),
+        ]),
+      ]);
+
+      // Clear the language context filter
+      await languageContext.clearLanguageContext();
+
+      expect(discovery.buildQueryTree()).toEqual([
+        new FileTreeDirectory(workspacePath, "workspace", env, [
+          new FileTreeLeaf(
+            join(workspacePath, "query1.ql"),
+            "query1.ql",
+            "java",
+          ),
+          new FileTreeLeaf(
+            join(workspacePath, "query2.ql"),
+            "query2.ql",
+            "python",
+          ),
+        ]),
+      ]);
+    });
   });
 
   describe("recomputeAllQueryLanguages", () => {