> After getting the results, i will filter them with Python filters,
> as i don't know how to filter many-to-many queries directly.
>
> Should i somehow make custom queries that handles many-to-many
> relationships etc. or is there something else i'm missing that
> makes the system slow? I have ran the bench with MySQL and
> PostgreSQL engines, the result is the same. When running with a
> profiler, at least ~90% of the time is taken by SQLAlchemy.

one general suggestion, try to move the filtering on the sql side; 
thus u'll have less data transferred then instantiated then 
filtered - which is probably eating most of the time.

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