How to Import Shopify Payouts and Transactions into QuickBooks
With Shopify Payments, your bank receives a payout every few days: orders paid by card, minus Shopify’s fees and any refunds or adjustments. The bank feed only shows that lump sum. To get the detail — and keep payouts matching your bank — import Shopify’s transactions. Two ways:
Option 1: Shopify Connector by QuickBooks (QuickBooks Online)
Intuit’s Shopify Connector app for QuickBooks Online imports orders, sales, refunds, fees and payouts so you can reconcile deposits. Product tracking (matching Shopify products to QuickBooks items by SKU and name) and customer tracking are optional. Imported transactions land in a review list before they are added to your books.
- In QuickBooks Online open Apps / Integrations, search for Shopify Connector and install it.
- Connect your Shopify store and choose the bank account where payouts arrive.
- Pick your options (products, customers) and the start date, then review the imported transactions.
Several third-party apps do the same with more options (multi-currency, inventory, other payment gateways); they are paid subscriptions.
Option 2: Shopify Payments CSV → QBO
For QuickBooks Desktop, without an app, or to catch up old months.
1. Export from Shopify
Shopify offers two useful exports (both CSV):
- Payouts list — one row per payout with Charges, Refunds, Adjustments, Reserved Funds, Fees and Total: Finance → Payouts → Export.
- Payout transactions — one row per transaction (Transaction Date, Type, Order, Payout Date, Amount, Fee, Net…). Open a single payout and export its transactions, or export all transactions from the Shopify Payments settings.
Column names can change over time and EU stores get a VAT column; the converter detects the common layouts.
2. Convert to QBO
- Drop the transactions CSV into the CSV to QBO converter. It uses Transaction Date, the Order number as description and Amount (the gross charge or refund). Switch the Amount column to Net if you want fees already deducted.
- Choose Checking as the account type and download the
.qbofile. - For the payouts list, the converter picks Payout Date and Total. Payouts leave Shopify, so they must be money out — tick Reverse signs if they show as positive.
3. Import into a Shopify clearing account
Create a Bank-type account Shopify Payments and import both files into it (QuickBooks Online: Banking → Link account ▾ → Upload from file; Desktop: File → Utilities → Import → Web Connect Files). Then:
- charges → Sales (or Shopify Sales),
- refunds → Refunds / Sales returns,
- fees (if you imported gross) → Merchant fees expense — import the Fee column as its own file, or post monthly fees as one journal entry,
- payouts → Transfer to your checking account, matching the deposit in your bank feed.
After each payout the clearing account returns to the amount still pending in Shopify.
Reconciling payouts
If a bank deposit doesn’t match a payout total:
- check Reserved funds and Adjustments in the payout (chargebacks, reserves, retried amounts);
- the payout may include transactions from several days;
- currency conversion can apply if you sell in other currencies.
Shopify’s payout reconciliation report (available with Shopify Payments) summarises transactions, fees and payouts for a date range and is useful for a month-end check.
Other payment methods
PayPal, Stripe, Amazon Pay and manual payments are not part of Shopify Payments payouts. Import them from their own accounts — see PayPal to QuickBooks and Stripe to QuickBooks.