diff --git a/extensions/ql-vscode/CHANGELOG.md b/extensions/ql-vscode/CHANGELOG.md
index 74a3f787393..e420de7a165 100644
--- a/extensions/ql-vscode/CHANGELOG.md
+++ b/extensions/ql-vscode/CHANGELOG.md
@@ -2,6 +2,8 @@
 
 ## [UNRELEASED]
 
+- Add a command _CodeQL: Run Query on Multiple Databases_, which lets users select multiple databases to run a query on. [#898](https://github.com/github/vscode-codeql/pull/898)
+
 ## 1.5.2 - 13 July 2021
 
 - Add the _Add Database Source to Workspace_ command to the right-click context menu in the databases view. This lets users re-add a database's source folder to the workspace and browse the source code. [#891](https://github.com/github/vscode-codeql/pull/891)
diff --git a/extensions/ql-vscode/package.json b/extensions/ql-vscode/package.json
index ee8f6aca9a4..837a8b23282 100644
--- a/extensions/ql-vscode/package.json
+++ b/extensions/ql-vscode/package.json
@@ -245,6 +245,10 @@
         "command": "codeQL.runQuery",
         "title": "CodeQL: Run Query"
       },
+      {
+        "command": "codeQL.runQueryOnMultipleDatabases",
+        "title": "CodeQL: Run Query on Multiple Databases"
+      },
       {
         "command": "codeQL.runRemoteQuery",
         "title": "CodeQL: Run Remote Query"
@@ -680,6 +684,10 @@
           "command": "codeQL.runQuery",
           "when": "resourceLangId == ql && resourceExtname == .ql"
         },
+        {
+          "command": "codeQL.runQueryOnMultipleDatabases",
+          "when": "resourceLangId == ql && resourceExtname == .ql"
+        },
         {
           "command": "codeQL.runRemoteQuery",
           "when": "config.codeQL.canary && editorLangId == ql && resourceExtname == .ql"
@@ -830,6 +838,10 @@
           "command": "codeQL.runQuery",
           "when": "editorLangId == ql && resourceExtname == .ql"
         },
+        {
+          "command": "codeQL.runQueryOnMultipleDatabases",
+          "when": "editorLangId == ql && resourceExtname == .ql"
+        },
         {
           "command": "codeQL.runRemoteQuery",
           "when": "config.codeQL.canary && editorLangId == ql && resourceExtname == .ql"
diff --git a/extensions/ql-vscode/src/extension.ts b/extensions/ql-vscode/src/extension.ts
index 89b7ad802e6..0f2f2f47be6 100644
--- a/extensions/ql-vscode/src/extension.ts
+++ b/extensions/ql-vscode/src/extension.ts
@@ -10,7 +10,8 @@ import {
   Uri,
   window as Window,
   env,
-  window
+  window,
+  QuickPickItem
 } from 'vscode';
 import { LanguageClient } from 'vscode-languageclient';
 import * as os from 'os';
@@ -29,7 +30,7 @@ import {
   QueryServerConfigListener
 } from './config';
 import * as languageSupport from './languageSupport';
-import { DatabaseManager } from './databases';
+import { DatabaseItem, DatabaseManager } from './databases';
 import { DatabaseUI } from './databases-ui';
 import {
   TemplateQueryDefinitionProvider,
@@ -467,16 +468,18 @@ async function activateWithInstalledDistribution(
     selectedQuery: Uri | undefined,
     progress: ProgressCallback,
     token: CancellationToken,
+    databaseItem: DatabaseItem | undefined,
   ): Promise<void> {
     if (qs !== undefined) {
-      const dbItem = await databaseUI.getDatabaseItem(progress, token);
-      if (dbItem === undefined) {
+      // If no databaseItem is specified, use the database currently selected in the Databases UI
+      databaseItem = databaseItem || await databaseUI.getDatabaseItem(progress, token);
+      if (databaseItem === undefined) {
         throw new Error('Can\'t run query without a selected database');
       }
       const info = await compileAndRunQueryAgainstDatabase(
         cliServer,
         qs,
-        dbItem,
+        databaseItem,
         quickEval,
         selectedQuery,
         progress,
@@ -549,13 +552,66 @@ async function activateWithInstalledDistribution(
         progress: ProgressCallback,
         token: CancellationToken,
         uri: Uri | undefined
-      ) => await compileAndRunQuery(false, uri, progress, token),
+      ) => await compileAndRunQuery(false, uri, progress, token, undefined),
       {
         title: 'Running query',
         cancellable: true
       }
     )
   );
+  interface DatabaseQuickPickItem extends QuickPickItem {
+    databaseItem: DatabaseItem;
+  }
+  ctx.subscriptions.push(
+    commandRunnerWithProgress(
+      'codeQL.runQueryOnMultipleDatabases',
+      async (
+        progress: ProgressCallback,
+        token: CancellationToken,
+        uri: Uri | undefined
+      ) => {
+        const quickPickItems = dbm.databaseItems.map<DatabaseQuickPickItem>(dbItem => (
+          {
+            databaseItem: dbItem,
+            label: dbItem.name,
+            description: dbItem.language,
+          }
+        ));
+        /**
+         * Databases that were selected in the quick pick menu.
+         */
+        const quickpick = await window.showQuickPick<DatabaseQuickPickItem>(
+          quickPickItems,
+          { canPickMany: true }
+        );
+        if (quickpick !== undefined) {
+          // Collect all skipped databases and display them at the end (instead of popping up individual errors)
+          const skippedDatabases = [];
+          const errors = [];
+          for (const item of quickpick) {
+            try {
+              await compileAndRunQuery(false, uri, progress, token, item.databaseItem);
+            } catch (error) {
+              skippedDatabases.push(item.label);
+              errors.push(error.message);
+            }
+          }
+          if (skippedDatabases.length > 0) {
+            void logger.log(`Errors:\n${errors.join('\n')}`);
+            void helpers.showAndLogWarningMessage(
+              `The following databases were skipped:\n${skippedDatabases.join('\n')}.\nFor details about the errors, see the logs.`
+            );
+          }
+        } else {
+          void helpers.showAndLogErrorMessage('No databases selected.');
+        }
+      },
+      {
+        title: 'Running query on selected databases',
+        cancellable: true
+      }
+    )
+  );
   ctx.subscriptions.push(
     commandRunnerWithProgress(
       'codeQL.runQueries',
@@ -611,7 +667,7 @@ async function activateWithInstalledDistribution(
         });
 
         await Promise.all(queryUris.map(async uri =>
-          compileAndRunQuery(false, uri, wrappedProgress, token)
+          compileAndRunQuery(false, uri, wrappedProgress, token, undefined)
             .then(() => queriesRemaining--)
         ));
       },
@@ -627,7 +683,7 @@ async function activateWithInstalledDistribution(
         progress: ProgressCallback,
         token: CancellationToken,
         uri: Uri | undefined
-      ) => await compileAndRunQuery(true, uri, progress, token),
+      ) => await compileAndRunQuery(true, uri, progress, token, undefined),
       {
         title: 'Running query',
         cancellable: true
diff --git a/extensions/ql-vscode/src/run-queries.ts b/extensions/ql-vscode/src/run-queries.ts
index 4a90532feb2..cd9a5429dce 100644
--- a/extensions/ql-vscode/src/run-queries.ts
+++ b/extensions/ql-vscode/src/run-queries.ts
@@ -563,7 +563,7 @@ export async function compileAndRunQueryAgainstDatabase(
   const dbSchemaName = path.basename(db.contents.dbSchemeUri.fsPath);
   if (querySchemaName != dbSchemaName) {
     void logger.log(`Query schema was ${querySchemaName}, but database schema was ${dbSchemaName}.`);
-    throw new Error(`The query ${path.basename(queryPath)} cannot be run against the selected database: their target languages are different. Please select a different database and try again.`);
+    throw new Error(`The query ${path.basename(queryPath)} cannot be run against the selected database (${db.name}): their target languages are different. Please select a different database and try again.`);
   }
 
   const qlProgram: messages.QlProgram = {