How to reconcile Stripe, Shopify, or Square sales in QuickBooks Online

If you collect payments through Stripe, Shopify, or Square, the money does not flow directly into your books the same way a bank transfer does. These platforms batch transactions, take fees, and deposit a net amount to your bank — which means you cannot just match the deposit to a single invoice. This article explains how to handle it correctly.

What You Will Need

• Access to QuickBooks Online
• Access to your Stripe, Shopify, or Square dashboard
• Your Mesa CPA bookkeeper (this setup is worth doing with them the first time)

Why This Is Different

When a client pays you directly via e-transfer, the full invoice amount hits your bank account. Simple.

When a client pays through Stripe, Shopify, or Square:

1. They pay the full amount to the platform
2. The platform deducts its fees
3. The platform deposits a net amount to your bank — often a batch of multiple transactions combined

So your bank statement shows one deposit that represents many sales, minus fees. If you just match that deposit to an invoice, you will have the wrong amount, missing fees, and potentially missing sales.

Normal Procedure

Option 1: Use the native QBO integration (recommended)

Stripe, Shopify, and Square all have direct integrations with QBO. When connected, the integration automatically:

• Imports each individual sale as an invoice or sales receipt
• Records the platform fee as an expense
• Matches the net deposit to your bank feed

To set up:

1. In QBO, go to Apps (in the left menu or at apps.intuit.com).
2. Search for your platform (Stripe, Shopify, or Square).
3. Follow the connection prompts — you will need to authorize access from within your platform account.
4. Configure the settings: which account to post sales to, which account to post fees to, and whether to sync historical data.

Once connected, transactions sync automatically going forward. Your Mesa CPA bookkeeper will validate the setup and confirm entries are posting to the right accounts.

Option 2: Manual reconciliation (if no integration)

If you are not using the native integration:

1. Download a payout report from your Stripe/Shopify/Square dashboard for the period.
2. The report shows each transaction, the fee, and the net payout.
3. Your bookkeeper creates a journal entry (or series of sales receipts) to record: gross sales as revenue, platform fees as an expense, net deposit as the bank transaction.
4. The net deposit in the bank feed gets matched to this entry.

This method works but is more time-consuming and error-prone than the integration. If you process more than a handful of transactions per month, set up the integration.

Abnormal Procedures

The integration is pulling in duplicate transactions.

This sometimes happens if your bank feed and the integration are both recording the same sale. Your Mesa CPA bookkeeper will need to turn off one source and clear the duplicates. Do not try to fix this yourself — it can create a bigger mess.

Your Stripe/Shopify payouts do not match your bank deposits.

Check whether the platform is holding a reserve (common with Stripe for new accounts) or whether there are chargebacks or refunds offsetting payouts. Cross-reference the payout report from the platform against your bank statement to find the difference.

You process sales in USD but your books are in CAD.

Multi-currency transactions need to be converted at the exchange rate on the date of the transaction. QBO handles this if multi-currency is enabled — but the setup needs to be done correctly. Talk to your Mesa CPA bookkeeper before you start recording USD transactions.

FAQ

Do I need to record every individual sale, or just the payout?

Ideally, every individual sale — this gives you accurate revenue data by product or service. The integration does this automatically. Manual reconciliation to just the payout is acceptable for simple setups but loses transaction-level detail.

How are platform fees treated for tax purposes?

Platform fees (Stripe processing fees, Shopify subscription and transaction fees, Square fees) are deductible business expenses. They should be recorded to a "Payment Processing Fees" or "Merchant Fees" account in your Chart of Accounts.

What about refunds issued through the platform?

Refunds processed through Stripe, Shopify, or Square are captured by the integration automatically. If you are reconciling manually, make sure refunds are recorded as reductions in revenue — not as expenses.

My accountant wants a sales breakdown by product. Can QBO do that?

Yes, if each sale is recorded with the correct product/service items. The integration typically maps products automatically. Run a Sales by Product/Service report in QBO (Reports > Sales and customers > Sales by Product/Service Summary).