Querying from Remote databases using an ORM ( ie. Eloquent )

I have recently come across a situation where querying from two tables that has about 16k records each.

Executing raw SQL results in the response time to a few seconds and if I opt to stick to the ORM queries , the same results in a nginx request timeout since the query takes more than 1 min to process.

Has anyone faced a similar scenario , I am aware that heavy queries can be made using a Doctrine.