Integration
Shopify Payments + Ottit

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.

100+Brands on this stack
EveryPayout tied to the bank deposit
15thFinancials by, often sooner
$595Ottit from, per month

Trusted by 100+ of your favorite DTC & CPG brands

01

How the data flows

Shopify Payments
Payments Shopify orders and refunds
Shopify Payments
Payments Shopify Payments payouts (net)
QuickBooks Online
Ledger Bookkeep entries into QBO or Xero
Bank Bank deposit matching
Output P&L on order date with fees separated
02

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.

Payout · Shopify Payments · 30 Sep 2026Reconciled by Ottit · Illustrative figures
LineDebitCredit
Bank deposit1000 · Operating checking12,526.06
Chargeback reserve1215 · Processor reserves180.00
Shopify Payments clearing1210 · Undeposited: Shopify12,706.06
Totals12,706.0612,706.06
The deposit matches the clearing balance to the cent; the reserve releases next cycle.✓ Reconciled by Ottit
03

Setup and monthly work

Pull payout detailBookkeep reads every Shopify Payments payout and its underlying orders, refunds, fees and adjustments.
Book on the order dateGross sales, discounts, shipping income and sales tax are recorded when the order is placed; fees when the payout settles.
Match the depositEach payout is matched to the bank deposit, including reserve holds, chargeback debits and Shop Capital remittances.
Handle the edge casesGift cards as a liability until redeemed, pre-orders as deferred revenue, Shop Capital as a loan, multi-currency at the payout's conversion.
Tie out monthlyShopify Finances summary versus the ledger, and Shopify Tax collected versus filed, before financials go out.

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.

Chad KrauseCo-Founder & CFO, TeraGanix · Sam's List
Chad Krause
04

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
Runs on Shopify Payments is one piece. Ottit works inside the rest.
QuickBooks OnlineQuickBooks Online
XeroXero
Bookkeep
Gusto
Bill.comBill.com
Ramp
Mercury
StripeStripe
QuickBooks OnlineQuickBooks Online
XeroXero
Bookkeep
Gusto
Bill.comBill.com
Ramp
Mercury
StripeStripe
"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."
Robert YangClient since 2023 · Sam's List · Google
"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."
Nathan GarrisonClient since 2022 · Sam's List
05

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.

Already on Shopify Payments? Let us look at the mapping.

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E-Commerce
Startups
SaaS
Advertisers
Marketing Agencies
IT Firms
CPG
App Developers
Pre Revenue
Fund Raising
E-Commerce
Startups
SaaS
Advertisers
Marketing Agencies
IT Firms
CPG
App Developers
Pre Revenue
Fund Raising
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Revenue Recognition
Analysis + Reporting
Reconciliation
Inventory Assets
COGS
Categorization
A/P + A/R
Data Entry
Historical Clean Ups
Revenue Recognition
Analysis + Reporting
Reconciliation
Inventory Assets
COGS
Categorization
A/P + A/R
Data Entry
Historical Clean Ups
Revenue Recognition
Analysis + Reporting
Reconciliation
Inventory Assets
COGS
Categorization
A/P + A/R
Data Entry
Historical Clean Ups