Comments - Mysql stored procedure is slower 20 times than standard query
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Asking how to stop a query affecting so many rows sounds like the wrong question. An UPDATE should have a well defined amount of rows affected by the query. Do you really need to update so many rows to achieve your business function?
I cannot guess how a SP time would be different to a direct query. If you can construct a repeatable test case to show this please create a bug report. If the direct query is doing it faster, then why not just use that?
Without details I cannot answer other performance questions.