Looking for the best way to make Shopify QuickBooks integration? In this guide you will learn how to connect your Shopify store to the Synder app.


  1. Start Shopify QuickBooks integration from scratch

  2. Connect Shopify to already existing account

  3. One-click Shopify QuickBooks setup (preferred)

  4. Step-by-Step Data Flow Setup (optional)

Once you set up the integration, the app will account for your Shopify payments in QuickBooks. When you integrate Shopify and QuickBooks, your inventory, orders, customers, and shipping are automatically updated and accurate. As soon as you integrate QuickBooks and Shopify stores within just a few clicks, all your most important features and tools – Shopify inventory, Shopify orders, Shopify customers, and Shopify shipping – become accurate and precise, as well as receive an automatic update.

If you are a Xero user, learn more about Shopify Xero integration.

Start Shopify QuickBooks integration from scratch

Important note 1: if you have manually created orders or Shopify POS (point of sale) orders, check out ‘How to sync Shopify manual order refunds’ and ‘How to sync Shopify POS orders’ guides respectively to learn how to set Synder to process them as well.

Important note 2: if your Shopify store accepts payments via different channels (e.g. PayPal, Stripe, etc.) you need to connect these payment platforms to Synder as well for the app to recognize all transactions and sync them successfully. Just click the Plus icon in the top-right corner and follow the already familiar steps. This will allow Synder to record Shopify fees amounts into your accounting company

Connect Shopify to already existing account

Once you’ve launched the Synder app and connected your accounting platform you will appear on Step 3: Connect your payment processor page.

If you already have your accounting company connected and you want to access this page follow the steps below:

1. Select Organization needed at the top right
2. Go to Settings on the left menu
3. Click on the Add payment platform button

Add sign in the upper-right corner and select Add Payment platform

To connect Shopify follow the steps below:

  1. Select Shopify in the dropdown on the Connect payment platform page
  2. Enter your Shopify store name in the tab below. Check what is the name of your store in your Shopify account (you can copy it from Shopify and paste it into Synder).
  3. Click Connect
Shopify Synder Integration

One-click setup (preferred)

Now you have done with the connections and you can proceed with the setup of the integration: you can go for either Option 1 (One-click setup) which is a recommended option and based on the flow the majority of the clients use. You will be able to get back to detailed settings at ANY time.

Step-by-Step Data Flow Setup (optional)

Alternatively, you can use Option 2 – a detailed step-by-step configuration, do this only if you know what you are doing. Learn more about customizable Stripe settings.

proceed with the setup

The flow of the app: From now on your Shopify transactions will be synchronized to the Shopify Bank Account – a clearing account automatically created by Synder in your Chart of Accounts for storing all of your Shopify transactions in one place. And once money payout happens, Synder will create a transfer to your checking account for easy reconciliation.

Details on the settings: You can enable the Apply taxes setting for Synder to recognize tax details in each Shopify transaction and record them to QuickBooks.
Payouts (Shopify transfers of funds to your bank) information will be automatically recorded to the Checking account for quick reconciliation. You are to select your checking account in the dropdown right at the one-click setup step.

Congratulations! You have set up the integration between Shopify and Synder! Now feel free to check how it works. 

In case of any questions contact our support team in the in-app chat, by phone or email in the footer of the page!

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