SP taking 15 minutes, but the same query when executed returns results in 1-2 minutes

Question

So basically I have this relatively long stored procedure. The basic execution flow is that it SELECTS INTO some data into temp tables declared with he #

Answer 1

I would suggest the issue is related to the type of temp table (the # prefix). This temp table holds the data for that database session. When you run it through your app the temp table is deleted and recreated.
You might find when running in SSMS it keeps the session data and updates the table instead of creating it. Hope that helps :)