Shopify + QuickBooks Online setup guide

Overview of Shopify + QuickBooks Online integration

Connect Shopify and QuickBooks to start syncing your daily sales transactions.

  • Sales and transfer sync
    • On a daily basis, the integration will sync a summary of your previous day’s sales data into QuickBooks Online generating an invoice or opt to sync each Shopify order into an individual QuickBooks Online invoice.
    • You can customise your preferred sales summary view choosing from a wide array of formats.
    • Capture all payment transactions including gift cards, tips, tax and payment fees.
    • Easily reconcile Shopify sales and payments in QuickBooks Online.

How to set up Shopify + QBO integration

  1. Register or sign in to the Amaka dashboard to get started.

  2. Click the New integration button and select Shopify + QuickBooks Online from the integrations list to commence the setup.

  3. Sign in to your Shopify account by clicking the Connect new account button underneath the Shopify logo. Follow the guided authentication process to grant all relevant permissions.

  4. Authenticate your QuickBooks Online account following the same procedure, then click Save + Continue.

  5. Follow the wizard to choose your preferred configuration method, invoice breakdown, invoice format, mapping and scheduler options to complete the setup of the integration.

  6. Click Save + Continue to finish and activate the integration.

If you have selected today’s date as your scheduled sync start date, your transactions will not appear in QuickBooks Online until tomorrow.

Configuration methods

At the beginning of your setup wizard, you’ll be able to choose your preferred configuration method from the options listed below.

Express configuration

Every day, an invoice with your daily sales summary will be created in QuickBooks Online.

The integration will automatically map sales and payments from Shopify into QuickBooks Online by creating the following default accounts:

Account and code mapping
Sales Type QBO Account QBO Account Type
Sales Shopify Sales Income
Discounts Shopify Discounts Income
Shipping/Delivery Fees Shopify Shipping/Delivery Fees Income
Shopify Fees Shopify Fees Expense
Tips Shopify Tips Other Current Liability
Gift Card Shopify Gift Card Other Current Liability
Adjustment Shopify Sales Income
Cost of Goods Sold Shopify COGS Cost of Goods Sold
Inventory Shopify Inventory Other Current Asset

For US regions only:

Transaction Type QBO Account and Product Name QBO Account Type
Sales Tax Shopify Collected Taxes Other Current Liability
Total sales tax amount is synced to a separate line within the generated invoice and mapped to the Shopify Collected Taxes by default. The Tax Exempt tax rate will be used as the tax rate for the transaction lines such as sales, discounts, shipping, etc.
Payment mapping
Payment Type QBO Account QBO Account Type
Shopify Payment Shopify Payment Balance Bank
Cash Shopify Cash Clearing Other Current Asset
Cash on Delivery (COD) Shopify Cash Clearing Other Current Asset
Gift Card Shopify Gift Card Other Current Liability
Exchange Credit Shopify Exchange Credit Clearing Other Current Liability
All Other Payment Types Shopify Other Payment Clearing Other Current Asset
Advanced setup

The advanced setup will allow you to choose your own custom mapping in relation to sales and payments in Shopify.

Recommended for professional bookkeepers and accountants.
Guided setup

Schedule a call with one of our Integration Specialists that will help you decide on the best configuration method for you and guide you through the setup.

Schedule a call now

FAQ on how to set up Shopify + QuickBooks Online

Find answers to the most frequently asked questions about this integration.

Yes! Using our integration, a summary of your previous day’s sales data is automatically synced from Shopify into QuickBooks Online as an invoice. This means you get perfectly reconciled accounts.

Amaka’s Shopify accounting integration works on Simple Start, the lowest tier plan available for QuickBooks Online.

Forever free plan available. Visit our pricing page to find out more about premium features.

Of course! If you would like to request a walkthrough or discuss the capabilities of the integration in more detail, you may schedule a support session with one of our integration experts.

Yes! The Shopify + QuickBooks Online integration by Amaka syncs both fees and Shopify payouts (what Shopify deposits into your bank account). Fees are synced to QuickBooks Online as a journal entry and payouts are synced to QuickBooks Online in a bank transfer.

For the Shopify + QuickBooks Online integration, you can choose to sync sales to a summarized invoice or to a categorized invoice. With a summarized invoice, total sales are synced into a single income account in QuickBooks Online. If you select a categorized invoice, you can map each Shopify product or location to a specific income account.

Sure, you can select the date that you wish the data to be synced from through the integration scheduler page.

With the Shopify + QuickBooks integration, your sales and fees are automatically accounted for with payouts reconciliation. There’s no need to manually match up transactions. In QuickBooks Online, select Banking and then For Review. Select the Recognised filter from the dropdown and find the transaction. From the Action column, select Match so that the transaction is matched in both accounts.

By regularly reconciling your data, you can ensure that the Shopify Payments data from Shopify matches up with the amount Shopify deposits into your bank account. You’ll be able to identify potential issues such as fraud, chargebacks and disputes before it’s too late.

In case you have revoked the access or changed credentials of an account used for an integration, you can easily reconnect it by expanding the options menu and clicking the Reconnect (or Edit) button in the Connected accounts page.

At any time, you can access your Amaka dashboard and disable an integration by either turning it OFF or deleting it entirely. You can follow the instructions here.

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