diff --git a/packages/lib/services/e2ee/EncryptionService.ts b/packages/lib/services/e2ee/EncryptionService.ts
index db9a52585..97cff6846 100644
--- a/packages/lib/services/e2ee/EncryptionService.ts
+++ b/packages/lib/services/e2ee/EncryptionService.ts
@@ -254,6 +254,7 @@ export default class EncryptionService {
 		model.created_time = now;
 		model.updated_time = now;
 		model.source_application = Setting.value('appId');
+		model.hasBeenUsed = false;
 
 		return model;
 	}
diff --git a/packages/lib/services/e2ee/types.ts b/packages/lib/services/e2ee/types.ts
index 564877acc..7899d1556 100644
--- a/packages/lib/services/e2ee/types.ts
+++ b/packages/lib/services/e2ee/types.ts
@@ -8,6 +8,7 @@ export interface MasterKeyEntity {
 	content?: string;
 	type_?: number;
 	enabled?: number;
+	hasBeenUsed?: boolean;
 }
 
 export type RSAKeyPair = any; // Depends on implementation
diff --git a/packages/lib/services/synchronizer/syncInfoUtils.test.ts b/packages/lib/services/synchronizer/syncInfoUtils.test.ts
index bbdb299e0..a0f813333 100644
--- a/packages/lib/services/synchronizer/syncInfoUtils.test.ts
+++ b/packages/lib/services/synchronizer/syncInfoUtils.test.ts
@@ -1,6 +1,6 @@
-import { afterAllCleanUp, setupDatabaseAndSynchronizer, switchClient, encryptionService } from '../../testing/test-utils';
+import { afterAllCleanUp, setupDatabaseAndSynchronizer, switchClient, encryptionService, msleep } from '../../testing/test-utils';
 import MasterKey from '../../models/MasterKey';
-import { masterKeyEnabled, setMasterKeyEnabled, SyncInfo, syncInfoEquals } from './syncInfoUtils';
+import { masterKeyEnabled, mergeSyncInfos, setMasterKeyEnabled, SyncInfo, syncInfoEquals } from './syncInfoUtils';
 
 describe('syncInfoUtils', function() {
 
@@ -92,4 +92,33 @@ describe('syncInfoUtils', function() {
 		}
 	});
 
+	it('should merge sync target info and takes into account usage of master key - 1', async () => {
+		const syncInfo1 = new SyncInfo();
+		syncInfo1.masterKeys = [{
+			id: '1',
+			content: 'content1',
+			hasBeenUsed: true,
+		}];
+		syncInfo1.activeMasterKeyId = '1';
+
+		await msleep(1);
+
+		const syncInfo2 = new SyncInfo();
+		syncInfo2.masterKeys = [{
+			id: '2',
+			content: 'content2',
+			hasBeenUsed: false,
+		}];
+		syncInfo2.activeMasterKeyId = '2';
+
+		// If one master key has been used and the other not, it should select
+		// the one that's been used regardless of timestamps.
+		expect(mergeSyncInfos(syncInfo1, syncInfo2).activeMasterKeyId).toBe('1');
+
+		// If both master keys have been used it should rely on timestamp
+		// (latest modified is picked).
+		syncInfo2.masterKeys[0].hasBeenUsed = true;
+		expect(mergeSyncInfos(syncInfo1, syncInfo2).activeMasterKeyId).toBe('2');
+	});
+
 });
diff --git a/packages/lib/services/synchronizer/syncInfoUtils.ts b/packages/lib/services/synchronizer/syncInfoUtils.ts
index 38a9ccc45..287ad915b 100644
--- a/packages/lib/services/synchronizer/syncInfoUtils.ts
+++ b/packages/lib/services/synchronizer/syncInfoUtils.ts
@@ -90,11 +90,32 @@ export function localSyncInfoFromState(state: State): SyncInfo {
 	return new SyncInfo(state.settings['syncInfoCache']);
 }
 
+const mergeActiveMasterKeys = (s1: SyncInfo, s2: SyncInfo, output: SyncInfo) => {
+	const activeMasterKey1 = getActiveMasterKey(s1);
+	const activeMasterKey2 = getActiveMasterKey(s2);
+	let doDefaultAction = false;
+
+	if (activeMasterKey1 && activeMasterKey2) {
+		if (activeMasterKey1.hasBeenUsed && !activeMasterKey2.hasBeenUsed) {
+			output.setWithTimestamp(s1, 'activeMasterKeyId');
+		} else if (!activeMasterKey1.hasBeenUsed && activeMasterKey2.hasBeenUsed) {
+			output.setWithTimestamp(s2, 'activeMasterKeyId');
+		} else {
+			doDefaultAction = true;
+		}
+	} else {
+		doDefaultAction = true;
+	}
+
+	if (doDefaultAction) {
+		output.setWithTimestamp(s1.keyTimestamp('activeMasterKeyId') > s2.keyTimestamp('activeMasterKeyId') ? s1 : s2, 'activeMasterKeyId');
+	}
+};
+
 export function mergeSyncInfos(s1: SyncInfo, s2: SyncInfo): SyncInfo {
 	const output: SyncInfo = new SyncInfo();
 
 	output.setWithTimestamp(s1.keyTimestamp('e2ee') > s2.keyTimestamp('e2ee') ? s1 : s2, 'e2ee');
-	output.setWithTimestamp(s1.keyTimestamp('activeMasterKeyId') > s2.keyTimestamp('activeMasterKeyId') ? s1 : s2, 'activeMasterKeyId');
 	output.setWithTimestamp(s1.keyTimestamp('ppk') > s2.keyTimestamp('ppk') ? s1 : s2, 'ppk');
 	output.version = s1.version > s2.version ? s1.version : s2.version;
 
@@ -110,6 +131,8 @@ export function mergeSyncInfos(s1: SyncInfo, s2: SyncInfo): SyncInfo {
 		}
 	}
 
+	mergeActiveMasterKeys(s1, s2, output);
+
 	return output;
 }
 
@@ -154,6 +177,14 @@ export class SyncInfo {
 		this.activeMasterKeyId_ = 'activeMasterKeyId' in s ? s.activeMasterKeyId : { value: '', updatedTime: 0 };
 		this.masterKeys_ = 'masterKeys' in s ? s.masterKeys : [];
 		this.ppk_ = 'ppk' in s ? s.ppk : { value: null, updatedTime: 0 };
+
+		// Migration for master keys that didn't have "hasBeenUsed" property -
+		// in that case we assume they've been used at least once.
+		for (const mk of this.masterKeys_) {
+			if (!('hasBeenUsed' in mk) || mk.hasBeenUsed === undefined) {
+				mk.hasBeenUsed = true;
+			}
+		}
 	}
 
 	public setWithTimestamp(fromSyncInfo: SyncInfo, propName: string) {