diff --git a/server/src/db/MongoDB.ts b/server/src/db/MongoDB.ts
index 8aea56279..59d2a32b7 100755
--- a/server/src/db/MongoDB.ts
+++ b/server/src/db/MongoDB.ts
@@ -35,6 +35,12 @@ class MongoDB implements IDb {
 					setDefaultsOnInsert: true,
 				}
 			);
+			// Run migrations BEFORE syncIndexes. The 0006 dedupe migration must run before
+			// the unique index on MonitorStats.monitorId is enforced, otherwise databases
+			// with stray duplicates (caused by the pre-fix race in updateRunningStats)
+			// will crash at startup when the unique index fails to build.
+			await runMigrations();
+
 			// Sync indexes
 			const models = mongoose.modelNames();
 			for (const modelName of models) {
@@ -47,8 +53,6 @@ class MongoDB implements IDb {
 				service: SERVICE_NAME,
 				method: "connect",
 			});
-
-			await runMigrations();
 		} catch (error: unknown) {
 			this.logger.error({
 				message: error instanceof Error ? error.message : "Unknown error",
diff --git a/server/src/db/migration/0006_cleanupDuplicateMonitorStatsForUniqueIndex.ts b/server/src/db/migration/0006_cleanupDuplicateMonitorStatsForUniqueIndex.ts
new file mode 100644
index 000000000..814b19776
--- /dev/null
+++ b/server/src/db/migration/0006_cleanupDuplicateMonitorStatsForUniqueIndex.ts
@@ -0,0 +1,78 @@
+import { MonitorStatsModel } from "../models/MonitorStats.js";
+import { logger } from "@/utils/logger.js";
+
+/**
+ * Second-pass dedupe of MonitorStats before the unique index on monitorId is enforced.
+ *
+ * 0003 ran the same dedupe, but the pre-fix race in StatusService.updateRunningStats
+ * could create new duplicates after 0003 completed. This migration re-runs the dedupe so
+ * the unique index added in the same PR can be built without failing.
+ *
+ * Keeps the document with the highest totalChecks for each monitorId (most data) and
+ * deletes the rest. Falls back to most recent updatedAt when totalChecks tie.
+ */
+export async function cleanupDuplicateMonitorStatsForUniqueIndex(): Promise<void> {
+	const SERVICE_NAME = "Migration:CleanupDuplicateMonitorStatsForUniqueIndex";
+
+	try {
+		logger.info({ service: SERVICE_NAME, message: "Starting pre-unique-index dedupe of MonitorStats" });
+
+		const duplicates = await MonitorStatsModel.aggregate([
+			{
+				$group: {
+					_id: "$monitorId",
+					docs: { $push: { id: "$_id", totalChecks: "$totalChecks", updatedAt: "$updatedAt" } },
+					count: { $sum: 1 },
+				},
+			},
+			{ $match: { count: { $gt: 1 } } },
+		]);
+
+		if (duplicates.length === 0) {
+			logger.info({ service: SERVICE_NAME, message: "No duplicate MonitorStats found" });
+			return;
+		}
+
+		logger.info({
+			service: SERVICE_NAME,
+			message: `Found ${duplicates.length} monitors with duplicate stats`,
+		});
+
+		let totalDeleted = 0;
+
+		type DocInfo = { id: string; totalChecks: number; updatedAt: Date };
+
+		for (const duplicate of duplicates) {
+			const monitorId = duplicate._id;
+			const docs: DocInfo[] = duplicate.docs;
+
+			// Sort by totalChecks desc, then updatedAt desc — keep the winner, delete the rest.
+			docs.sort((a, b) => {
+				const checksDiff = (b.totalChecks ?? 0) - (a.totalChecks ?? 0);
+				if (checksDiff !== 0) return checksDiff;
+				return new Date(b.updatedAt).getTime() - new Date(a.updatedAt).getTime();
+			});
+
+			const toDelete = docs.slice(1).map((doc) => doc.id);
+
+			if (toDelete.length > 0) {
+				const result = await MonitorStatsModel.deleteMany({ _id: { $in: toDelete } });
+				totalDeleted += result.deletedCount ?? 0;
+
+				logger.debug({
+					service: SERVICE_NAME,
+					message: `Deleted ${result.deletedCount} duplicate stats for monitor ${monitorId}`,
+				});
+			}
+		}
+
+		logger.info({
+			service: SERVICE_NAME,
+			message: `Cleanup complete. Deleted ${totalDeleted} duplicate MonitorStats documents`,
+		});
+	} catch (error) {
+		const errorMessage = error instanceof Error ? error.message : String(error);
+		logger.error({ service: SERVICE_NAME, message: `Error during MonitorStats dedupe: ${errorMessage}` });
+		throw error;
+	}
+}
diff --git a/server/src/db/migration/index.ts b/server/src/db/migration/index.ts
index f1a672af9..5b74a96fc 100644
--- a/server/src/db/migration/index.ts
+++ b/server/src/db/migration/index.ts
@@ -4,6 +4,7 @@ import { cleanupDuplicateMonitorStats } from "./0003_cleanupDuplicateMonitorStat
 import { fixInfrastructureThresholds } from "./0004_fixInfrastructureThresholds.js";
 import MigrationModel from "../models/Migration.js";
 import { migrateStatusPageTypeToArray } from "./0005_migrateStatusPageTypeToArray.js";
+import { cleanupDuplicateMonitorStatsForUniqueIndex } from "./0006_cleanupDuplicateMonitorStatsForUniqueIndex.js";
 import type { ILogger } from "@/utils/logger.js";
 
 type MigrationEntry = {
@@ -17,6 +18,7 @@ const migrations: MigrationEntry[] = [
 	{ name: "0003_cleanupDuplicateMonitorStats", execute: cleanupDuplicateMonitorStats },
 	{ name: "0004_fixInfrastructureThresholds", execute: fixInfrastructureThresholds },
 	{ name: "0005_migrateStatusPageTypeToArray", execute: migrateStatusPageTypeToArray },
+	{ name: "0006_cleanupDuplicateMonitorStatsForUniqueIndex", execute: cleanupDuplicateMonitorStatsForUniqueIndex },
 ];
 
 const runMigrations = async (logger?: ILogger) => {