Before You Start

This guide assumes you have administrator access to both QuickBooks Online and Shopify. You’ll also need your chart of accounts ready.

Overview

15 min
Setup Time
Basic
Difficulty
Monthly
Maintenance

What You’ll Learn

  • How to prep your QuickBooks accounts for clean syncs
  • Setting up A2X for automated daily syncs
  • Mapping taxes and fees correctly
  • Reconciling Shopify payouts with bank deposits

1. Preparation Steps

Before connecting anything, you need these accounts in QuickBooks:

Required Accounts

  • Shopify Sales (Income)
  • Shopify Fees (Expense)
  • Shopify Payouts (Bank/Asset)
  • Sales Tax Payable (Liability)

Optional (but recommended)

  • Shopify Refunds (Expense)
  • Shopify Discounts (Income Reduction)
  • Shopify Gift Cards (Liability)

2. Choosing Your Sync Method

You have two main options, each with serious pros and cons.

Method A: The Official “QuickBooks Online” App

This is the free app built by Intuit.

Pros:
  • It’s free.
  • Good for simple setups.
  • Imports sales as a summary.
Cons:
  • Lacks granular control.
  • Inventory sync is basic.
  • Can be hard to troubleshoot.

Method B: Third-Party Connectors (A2X, Bold)

These are paid apps that offer far more control.

Expert Tip: We strongly recommend using a third-party connector like A2X. It uses the “settlement” or “payout” method, which perfectly matches the bank deposits from Shopify, making reconciliation a one-click process.

3. Step-by-Step: Syncing with A2X

Here is the high-level workflow for a clean setup.

Diagram showing data flow from Shopify through A2X to QuickBooks Online for automated bookkeeping

This is how data should flow: from Shopify, processed by a tool like A2X, then sent to QuickBooks.

Here is a sample code block to show how an API call might look.

{
  "order_id": 12345,
  "customer": "John Doe",
  "total": 115.00,
  "line_items": [
    { "sku": "QB-SH-BOOK", "quantity": 1 }
  ]
}

4. Setting Up A2X

  1. 1

    Connect Shopify to A2X

    Authorize A2X to access your Shopify store. Use the same email as your QuickBooks account.

  2. 2

    Connect A2X to QuickBooks

    Link your QBO account in A2X settings. Grant admin access when prompted.

  3. 3

    Map Your Accounts

    Assign your Shopify sales, fees, and payouts to the correct QBO accounts.

Common Error: Wrong Account Type

Make sure your Shopify Payouts account is set as a Bank account type in QuickBooks, not Income or Asset. This ensures proper reconciliation.

5. Testing Your Setup

Test Import Checklist

  • Import a test payout from last month
  • Verify all amounts match Shopify
  • Check tax calculations are correct
  • Confirm bank deposit amounts align

Need Help?

Get Support

Having trouble with your setup? Our team can help troubleshoot your specific workflow.

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