diff --git a/src/mapeo-manager.js b/src/mapeo-manager.js
index 94e451f7..bc97493e 100644
--- a/src/mapeo-manager.js
+++ b/src/mapeo-manager.js
@@ -4,7 +4,6 @@ import { KeyManager } from '@mapeo/crypto'
 import Database from 'better-sqlite3'
 import { eq } from 'drizzle-orm'
 import { drizzle } from 'drizzle-orm/better-sqlite3'
-import { migrate } from 'drizzle-orm/better-sqlite3/migrator'
 import Hypercore from 'hypercore'
 import { TypedEmitter } from 'tiny-typed-emitter'
 import pTimeout from 'p-timeout'
@@ -26,6 +25,7 @@ import {
 } from './schema/client.js'
 import { ProjectKeys } from './generated/keys.js'
 import {
+  ExhaustivenessError,
   deNullify,
   getDeviceId,
   keyToId,
@@ -35,6 +35,7 @@ import {
   projectKeyToPublicId,
 } from './utils.js'
 import { openedNoiseSecretStream } from './lib/noise-secret-stream-helpers.js'
+import { migrate } from './lib/drizzle-helpers.js'
 import { omit } from './lib/omit.js'
 import { RandomAccessFilePool } from './core-manager/random-access-file-pool.js'
 import BlobServerPlugin from './fastify-plugins/blobs.js'
@@ -152,7 +153,28 @@ export class MapeoManager extends TypedEmitter {
         : path.join(dbFolder, CLIENT_SQLITE_FILE_NAME)
     )
     this.#db = drizzle(sqlite)
-    migrate(this.#db, { migrationsFolder: clientMigrationsFolder })
+
+    const indexedTables = [projectSettingsTable]
+
+    const migrationResult = migrate(this.#db, {
+      migrationsFolder: clientMigrationsFolder,
+    })
+    let reindex
+    switch (migrationResult) {
+      case 'initialized database':
+      case 'no migration':
+        reindex = false
+        break
+      case 'migrated':
+        reindex = true
+        break
+      default:
+        throw new ExhaustivenessError(migrationResult)
+    }
+
+    if (reindex) {
+      for (const table of indexedTables) this.#db.delete(table).run()
+    }
 
     this.#localPeers = new LocalPeers({ logger })
     this.#localPeers.on('peers', (peers) => {
@@ -165,7 +187,7 @@ export class MapeoManager extends TypedEmitter {
     })
 
     this.#projectSettingsIndexWriter = new IndexWriter({
-      tables: [projectSettingsTable],
+      tables: indexedTables,
       sqlite,
       logger,
     })