The EXPLAIN verb can be used to show you the “execution plan” of any SQL statement ... this being the actual sequence of low-level operations that the query engine will carry out in order to do what the query says to do.   It is often the case that “there’s more than one way to do it,” but that one of them will be noticeably better than the others.

You can obtain slight speedups by “preparing a statement-handle” once, then using it to execute the same query multiple times, changing the set of parameters that you give it each time.

How many queries-per-second are you running, and what sort of queries are they?   Are the tables InnoDB?   Transactions?