First, make sure you are profiling the performance properly. For example, run the query twice from ADO.NET and see if the second time is much faster than the first time. This removes the overhead of waiting for the app to compile and the debugging infrastructure to ramp up.
Next, check the default settings in ADO.NET and SSMS. For example, if you run SET ARITHABORT OFF in SSMS, you might find that it now runs as slow as when using ADO.NET.
What I found once was that SET ARITHABORT OFF in SSMS caused the stored proc to be recompiled and/or different statistics to be used. And suddenly both SSMS and ADO.NET were reporting roughly the same execution time. Note that ARITHABORT is not itself the cause of the slowdown, it’s that it causes a recompilation, and you are ending up with two different plans due to parameter sniffing. It is likely that parameter sniffing is the actual problem needing to be solved.
To check this, look at the execution plans for each run, specifically the sys.dm_exec_cached_plans table. They will probably be different.
Running ‘sp_recompile’ on a specific stored procedure will drop the associated execution plan from the cache, which then gives SQL Server a chance to create a possibly more appropriate plan at the next execution of the procedure.
Finally, you can try the “nuke it from orbit” approach of cleaning out the entire procedure cache and memory buffers using SSMS:
DBCC DROPCLEANBUFFERS
DBCC FREEPROCCACHE
Doing so before you test your query prevents usage of cached execution plans and previous results cache.