How to Reconcile Amazon and Shopify Payouts in QuickBooks

You see deposits in your bank account from Amazon or Shopify-but they rarely match your sales reports. That’s because fees, refunds, and timing all affect your payouts. Here’s how to reconcile it all in QuickBooks the right way.

Step-by-Step Reconciliation Process

1. Download Reports

• Amazon: Settlement reports from Seller Central
• Shopify: Payout reports via Payments dashboard

2. Create a Clearing Account

Set up a “Shopify Clearing” or “Amazon Clearing” account in QuickBooks. Record gross sales here before subtracting fees.

3. Match Deposits to Reports

Each payout = sales – refunds – chargebacks – processing fees. Enter these components to explain the deposit fully.

4. Reconcile Monthly

Ensure the ending balance in your clearing account equals zero once all payouts for that period are booked.

Test Case

A Shopify + Amazon seller came to us with 6 months of unreconciled books. We:

• Created clearing accounts
• Imported historical payout data
• Balanced all deposits by platform within 14 days

They now get clear monthly financials that tie out to the penny.

Tax Relevance

Accurate reconciliation ensures:

• Correct 1099-K income reporting
• Deductible transaction fees
• Sales tax liability calculations by platform

Need help reconciling your ecommerce payouts? Our QuickBooks ecommerce bookkeeping team can do it all for you.

Ecommerce Bookkeeping for Amazon & Shopify Sellers Across States

• California
• Texas
• Florida
• New York
• Illinois

Ecommerce Bookkeeping for Amazon & Shopify Sellers Across Key ZIPs

• 90001 (Los Angeles)
• 77001 (Houston)
• 33101 (Miami)
• 10001 (New York)
• 60601 (Chicago)

View All ZIP Codes →

FAQs

Do I need separate clearing accounts for each platform?

Yes. It keeps reconciliation clean and allows platform-level profitability reporting.

What if I don’t use QuickBooks?

We also support Xero and FreshBooks users with ecommerce reconciliation needs.

Do you help set this up for me?

Yes. We can configure your chart of accounts and create automation workflows where possible.

Let RemoteBooksOnline reconcile your Amazon and Shopify books accurately and automatically.

Book your ecommerce reconciliation consultation today