What does MariaDB do at midnight? Does MariaDB do anything in particular at midnight and lasts for 1.5 hrs? 

I've noticed this over the past week that mysqld uses 100% CPU and 75% RAM usage slowing down the rest of my applications. 

Looking at the current connections there is no slow queries or similar happening at this time.

This is 50GB InnoDB database with >2500 tables 

What can I do to troubleshoot what is going on at this time of day? The rest of my application grinds to halt and critical processes cannot work fast enough as mysqld hogs the resources.

Thanks,
Hi user1202278 (is that your real name?),

MariaDB does not perform any particular scheduled actions on its own.  There is almost certainly a cron job at work, unless there are users who stay up late every night!

It would be a good exercise to monitor your DB for a while and see how often and when heavy processes are running.  From there, you can narrow down the suspects.  If you haven't already, I would recommend that you invest a good monitoring tool.  I personally use Navicat Monitor for MySQL/MariaDB.  It provides all of the important stats on the Dashboard page and can track server metrics such as disk usage, I/O, CPU, RAM, etc.

It has a 14 day trial, which should be plenty of time to diagnose your issue.

Best of luck!