I think, startup only run once the server start, you should be looking at crons instead. Either use some packages like: https://github.com/percolatestudio/meteor-synced-cron/ or put Metoer.setInterval if it is not critical.
I think a better solution is to use a MongoDB TTL index. MongoDB will automatically delete documents older than given time. For your case the mongo command will look like this.
For more info checkout MongoDB Docs on TTL indexes. You can also create the index at meteor app startup. (I didn’t test these codes if they didn’t work but it’ll be something very similar).
// on server
Meteor.startup(function () {
Entries._ensureIndex({createdAt: 1}, {expireAfterSeconds: 60*60*24*90});
});