February 10, 2026
Why your Stripe and PayPal deposits never match your invoices
You invoiced a client for $1,200. A few days later, $1,165.20 shows up in your bank account. That's not a partial payment — it's Stripe taking its cut before depositing the rest. But now your invoice says $1,200 and your bank says $1,165.20, and nothing lines up.
This is the single biggest reason invoice reconciliation is painful for small businesses. Here's how the math works across the most common payment processors.
Stripe: 2.9% + $0.30 per transaction
Stripe's standard pricing for online card payments is 2.9% of the transaction amount plus $0.30. On a $1,200 invoice, that's $35.10 in fees, leaving you with $1,164.90. On a $500 invoice, Stripe takes $14.80, depositing $485.20.
But it gets more complicated. Stripe often batches multiple payments into a single bank deposit. So instead of seeing five separate deposits that you can match individually, you get one lump sum that represents Tuesday's payments minus Tuesday's fees. Now you need Stripe's payout report to break it down — another spreadsheet to cross-reference.
PayPal: 3.49% + $0.49 (and it varies)
PayPal's fee structure is less predictable. Standard commercial rates are 3.49% + $0.49 for online card payments, but rates differ for PayPal balance transfers, international payments, and micropayments. A $1,200 invoice paid via PayPal card costs $42.37 in fees, leaving $1,157.63 — a different amount than the same invoice paid through Stripe.
If the same client pays some invoices via PayPal and others via Stripe, you now have two different fee structures producing two different deposit amounts for identical invoice amounts. Good luck keeping that straight in a spreadsheet.
ACH and wire transfers: hidden intermediary fees
ACH transfers are often cheaper — many banks charge a flat fee of $0.20–$1.50 per transaction, or nothing at all. But wire transfers, especially international ones, are a different story. Your bank might charge $15–$30 to receive a domestic wire. International wires can lose $25–$50 in intermediary bank fees, plus currency conversion spreads.
A $5,000 invoice paid by international wire might arrive as $4,847.33 — and there's no standard formula to calculate backwards, because the intermediary fees aren't published or predictable.
The compounding problem
Here's what makes this genuinely hard: most small businesses accept payments through multiple channels. Client A pays via Stripe. Client B sends a PayPal payment. Client C does an ACH transfer. Each channel has different fees, different timing, and different bank descriptions.
Now multiply that across 50 invoices per month. Every single deposit needs a different fee calculation depending on how the client paid. You can't just subtract a flat percentage — you need to know the processor, the payment method, and sometimes the client's country to figure out what the fee should have been.
A better approach
The fee problem is mathematical — which means it's solvable by software, not spreadsheets. If a tool knows Stripe's fee structure and can see both your invoice amount and your deposit amount, it can calculate whether the deposit matches the invoice after fees. No manual math needed.
That's exactly what InvoiceTally does. It accounts for processor fees automatically when matching invoices to bank deposits — whether the payment came through Stripe, PayPal, ACH, or wire transfer.