diff --git a/extensions/ql-vscode/CHANGELOG.md b/extensions/ql-vscode/CHANGELOG.md
index 70d73a96037..6667433dffe 100644
--- a/extensions/ql-vscode/CHANGELOG.md
+++ b/extensions/ql-vscode/CHANGELOG.md
@@ -3,8 +3,8 @@
 ## [UNRELEASED]
 
 - Remove ability to download databases from LGTM. [#1467](https://github.com/github/vscode-codeql/pull/1467)
-- Removed the ability to manually upgrade databases from the context menu on databases. Databases are non-destructively upgraded automatically so 
-  for most users this was not needed. For advanced users this is still available in the Command Palette. [#1501](https://github.com/github/vscode-codeql/pull/1501)
+- Removed the ability to manually upgrade databases from the context menu on databases. Databases are non-destructively upgraded automatically so for most users this was not needed. For advanced users this is still available in the Command Palette. [#1501](https://github.com/github/vscode-codeql/pull/1501)
+- Always restart the query server after a manual database upgrade. This avoids a bug in the query server where an invalid dbscheme was being retained in memory after an upgrade. [#1519](https://github.com/github/vscode-codeql/pull/1519)
 
 ## 1.6.12 - 1 September 2022
 
@@ -20,7 +20,7 @@ No user facing changes.
 
 No user facing changes.
 
-## 1.6.9 - 20 July 2022 
+## 1.6.9 - 20 July 2022
 
 No user facing changes.
 
diff --git a/extensions/ql-vscode/src/upgrades.ts b/extensions/ql-vscode/src/upgrades.ts
index a7427c10abc..7ef3867f0f4 100644
--- a/extensions/ql-vscode/src/upgrades.ts
+++ b/extensions/ql-vscode/src/upgrades.ts
@@ -194,7 +194,14 @@ export async function upgradeDatabaseExplicit(
       void qs.logger.log('Running the following database upgrade:');
 
       getUpgradeDescriptions(compileUpgradeResult.compiledUpgrades).map(s => s.description).join('\n');
-      return await runDatabaseUpgrade(qs, dbItem, compileUpgradeResult.compiledUpgrades, progress, token);
+      const result = await runDatabaseUpgrade(qs, dbItem, compileUpgradeResult.compiledUpgrades, progress, token);
+
+      // TODO Can remove the next lines when https://github.com/github/codeql-team/issues/1241 is fixed
+      // restart the query server to avoid a bug in the CLI where the upgrade is applied, but the old dbscheme
+      // is still cached in memory.
+
+      await qs.restartQueryServer(progress, token);
+      return result;
     }
     catch (e) {
       void showAndLogErrorMessage(`Database upgrade failed: ${e}`);