You're going to get this problem as a general issue in any scalable application where crons cannot / should not run multiple times. It's not really AWS specific. I'm not sure to what extent you want to keep things coupled or how your crons are currently run but here are a few suggestions that might work for you:
Create a "cron runner" instance with a limit to run crons on
You could create a separate ECS service which has no autoscaling and a fixed value of 1 instance. This instance would run the same copy of your code as your "normal" instances and would run crons. You would turn crons off on your "normal" instances. You might find that this can be a very small instance since it doesn't handle any web traffic.
Create a "cron trigger" instance which fires off crons remotely
Here you create one "trigger" instance which sends a request to your normal instances through an ALB. Because your ALB will route the request to 1 of the servers behind it the cron only gets run once. One watch out with this is that if your cron is long running, you may need to consider your request timeouts. You'll also have to think about retries etc but I assume you already have a process that can be adapted for that.
The above solutions can be adapted with message queues etc but the basis of both is that there is another instance of some kind which starts the cron and is separate from your normal servers. Depending on when your cron runs, you may only need to run this cron instance for a few hours per day so it can be cost efficient to do things like this.
Personally I have used both methods in a multi-tenant application and I had to go with the option of running the cron like this due to the number of tenants and the time / resource it took to run the crons for all of them at once:
- Cloudwatch schedule triggers a lambda which sends a message to SQS to queue a cron for each tenant individually.
- Cron servers (totally separate from main web servers but running same / similar code) pull messages and run the cron for each tenant individually. Stores a key in redis for crons which are vital to only run once to stop issues with "at least once" delivery so crons don't run twice.
This can also help handle failures with retry policies and deadletter queues managed in SQS.
Ultimately you need to kick off these crons from one place. If possible, change up your crons so it doesn't matter if they run twice. It makes it easier to deal with retries and things like that.