Shopify Payments + Ottit
Shopify Payments, reconciled to the penny
Shopify Payments is Shopify's native processor; card rates run from 2.9% + 30¢ on Basic to 2.25% + 30¢ on Plus, and payouts arrive net of fees, refunds, chargebacks, reserves and Shop Pay Installments charges. Ottit reconciles each payout to its orders in QuickBooks Online or Xero through Bookkeep, books gift card sales and Shop Capital as liabilities, and ties Shopify Tax to what is remitted.
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How the data flows
One day in the ledger
What a single entry looks like in your ledger once Ottit has mapped it. One line per component, so margin by channel and the balance sheet fall out of the books instead of a spreadsheet.
| Line | Debit | Credit |
|---|---|---|
| Bank deposit1000 · Operating checking | 12,526.06 | |
| Chargeback reserve1215 · Processor reserves | 180.00 | |
| Shopify Payments clearing1210 · Undeposited: Shopify | 12,706.06 | |
| Totals | 12,706.06 | 12,706.06 |
Setup and monthly work
They helped us migrate TeraGanix's books from QuickBooks Desktop to QuickBooks Online from a really chunky instance to a clean, modernized tech stack with clean books that we receive in timely manner.

Who it's for
- 4.1Shopify and Shopify Plus brands whose bank deposits do not match Shopify sales
- 4.2Stores using Shop Pay Installments, gift cards, pre-orders or Shopify Capital
- 4.3Brands selling in multiple currencies through Shopify Markets
- 4.4Anyone who wants the P&L to agree with the Shopify Finances summary


"Amazing bookkeeping agency! really understand ecom and very granular about different channels and contrarevenue accounts which can get very complicated across the sheer transaction volume necessary in ecom."
"They've established a direct link between every platform where products are sold and our accounting system so that sales are reflected in real time."
Questions
Why is my Shopify payout smaller than my sales?
Fees, refunds, chargebacks, reserves, Shop Pay Installments fees and Shop Capital remittances are all netted out before the payout. Booking the payout as revenue understates sales and hides fees.
How are Shopify Payments fees recorded?
As a merchant processing expense on the payout date, separated from third-party gateway fees (PayPal, Klarna, Affirm) and app subscriptions, so contribution margin is real.
What about the third-party transaction fee?
If you use an outside gateway instead of Shopify Payments, Shopify charges 2% on Basic, 1% on Grow, 0.6% on Advanced and 0.2% on Plus. Ottit books it as its own line so it is visible.
Does Shopify Tax file for me?
Shopify Tax calculates and collects; filing and remittance are separate (Shopify offers it as a paid add-on). Ottit reconciles collected versus remitted every month regardless of who files.
Keep reading
Already on Shopify Payments? Let us look at the mapping.
A free 30-minute health check with a written read-out.