Can I base S-Corp taxes on my bank account cash flow and ignore my payment processor?

[T1SanDiego]

I use Stripe as my payment processor.  It takes customer money and holds it there.  When the services are provided (we sell travel bookings), only then do we distribute money to our bank account, usually after first paying ~75% to the service provider (which we usually can pay out right from Stripe via bank transfer) and after credit card fees.  We also do a lot of refunds.  

I'd like to be able to base taxable income/profit off of our bank account cash flows, just because it's more straightforward.  A large percentage of customer payments never make it to us because they flow to the service provider or are refunded.  Is there anyway to base our taxes on just our bank account revenues/expenses for 2017 and ignore our payment processor revenues (which also, by the way, sit for weeks if not months before we see them)?

I'm concerned that the 1099-K doc that Stripe will provide the IRS will overinflate our revenues and trigger a big red flag.  It might be more than double the revenues that make it to our bank account.

Thanks for any guidance!

[Rick19744 · Accepted solution]

The IRS will definitely be looking to match the 1099-K amount; that's the whole purpose behind filing those forms so the government can match both sides of the equation.

Having said that, this is only one part of the puzzle; the gross amount.  This gross amount will be reported on line 1 of your 1120S.  You will then report all your expenses on the applicable lines 7-19.  This will then provide you with your appropriate net income.  This should also provide you with the same result as if you were using your bank records.