Payment Processing in private practice

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Guess I'll just have to do the math, but I was just figuring that whether the money goes to a business expense, and then is deducted from business income and paid for by Uncle Sam (I'm sole prop/pass through), or it's a lower cost, would make little difference. Guess I'm wrong!

Say your sole prop generated $100k in credit card revenue. If 3% is your credit card fee, you earn $97k profit. You are taxed on $97k. If 2% is your credit card fee, you earn $98k and are taxed on $98k. It’s a business deduction, so you are never taxed on the $100k. Lowering fees 1% on this example still put $1k back into my pocket.