Paying Shopify fees and the Stripe Fee too, help!

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Hi there, 


We have just had a new Shopify store built and set up Shopify Payments. We used to use Stripe on our wordpress store.


We have just noticed we are paying fees twice on all our orders. We are paying Shopify fees and then for some reason we are paying paid through Stripe and being charged their fees as well. 


How do we stop this happening?