Looking for an easy way to communicate your Shopify stores with Synder accounting, QuickBooks or Xero company? With Shopify integration by Synder all your sales and expenses will be automatically recorded and prepared for one-click reconciliation in your QuickBooks or Xero (learn more about our automatic bank reconciliation feature for Xero in this article). The software allows multi-currency accounting for your Shopify payments and Shopify orders paid via alternative payment providers like Stripe, PayPal, Amazon Pay, etc., providing you with accurate records of your Shopify sales along with processing fees, taxes, customers, discounts, and other transaction details. Synder will help you track inventory in Synder accounting, QuickBooks or Xero and categorize all synced data automatically to keep your books up-to-date and precise.
Excited? Let’s connect your Shopify store to Synder and automate your books!
Overview:
Important note 1: If your Shopify store accepts payments via different channels other than Shopify Payments (e.g. PayPal, Stripe, etc.) you need to connect these payment platforms to Synder as well for the software to recognize all transactions and sync them successfully.
Important note 2: If you manually create and mark orders as “paid”, have Shopify POS (point of sale) orders, or receive payments via alternative payment providers that are not supported by Synder directly, check out how to sync Shopify manual orders, Shopify POS orders and Shopify Other Orders guides respectively to learn how to set Synder to process them as well.
Start the Shopify integration from scratch
- Create an account
If you’re getting started with Synder you’ll need to create a free Trial account and connect your accounting system first. Check out this guide if you would like to integrate Stripe with Synder accounting, QuickBooks Online or Xero and this article to connect your QuickBooks Desktop company.
Select the product(s) you are going to use:
- Synder Sync;
- Sales Analytics;
- Or both of them for perfect control of your business.

Synder Sync: choose this product to push all of your transaction data from all sales channels into QuickBooks Online, QuickBooks Desktop, Xero, or Synder Books – our native accounting solution.
Sales Analytics: this Synder product lets you see how your business is doing. It aggregates data across all of your connected sales channels and payment gateways and provides you with timely insights into your products’ performance and your customer behaviors, as well as financial health indicators such as total sales, average order value, etc. The data is updated every hour!
- Set up your Organization
Going through the set-up process of an Organization for your QuickBooks/Xero company or Synder Books – just fill in the information about your business and hit the Next step button.

- Select the platforms you would like to integrate
Now you need to select the platforms you would like to connect to Synder. Select Shopify and all other sales platforms you would like to integrate with Synder (click View all processors to see the list of all available platforms).

Note: Select all the services you are using to receive payments.You will be able to connect all of them right away or skip the connection of particular integrations and set them up any time later.
- Select and connect your accounting platform
Select your QuickBooks Online or Xero company by clicking on the Connectbutton and grant permission to the software to record data in your QuickBooks or Xero company or proceed with our own Synder Books.

Note 1: if you are a QuickBooks Desktop user, check out this video tutorial to learn How to connect and sync data into QuickBooks Desktop.
Note 2: check out this guide if you would like to integrate QuickBooks Online or Xero.
If you’re going to connect Synder Books, follow the steps on the screen to grant permission to the system
- Connect your Shopify store
Almost there! To complete the setup you just need to connect your Shopify and other sales platforms to Synder. You can integrate them one by one straight away following the steps on the screen: Copy your Shopify store name in format name.myshopify.com, not custom, and paste to Synder → hit Connect.

- Set up the Shopify integration
To complete the setup for the Shopify integration choose an account for payouts (usually, your Checking account) that will allow smooth reconciliation of your Shopify transactions in one click. Hit Continue to finish the configuration.
Connect Shopify to an already existing account
If you already have a Synder account and would like to integrate one more Shopify store follow the steps below:
- Switch to the needed Organization in the top-left corner of the Synder page.
- Navigate to Settings on the left-side menu.
- In the Iintegrations section click Add payment platform – > select Shopify in the dropdown and hit the Connect button
4. To complete the setup for the Shopify integration choose an account for payouts (usually, your Checking account) that will allow smooth reconciliation of your Shopify transactions in one click. Hit Continue to finish the configuration.

Tips and tricks on Shopify integration
Note 1: Shopify transactions will be synchronized to the Shopify (required for Synder) 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.
Note 2. If you accept payments via Shopify Payments you only need to connect your Shopify store to Synder. If you use some alternative payment gateways (e.g. Stripe, PayPal, Amazon Pay, etc.) it is strongly recommended to connect all payment providers to Synder in order to get flawless and automated records of sales, fees, refunds, and payouts from those payment platforms with additional information provided by Shopify orders.
Congratulations! Now as you set up the Shopify integration check out our 3 Must-Watch beginner guides to find out how Synder can help you automate your bookkeeping.
Get in touch with the Synder team via online chat, phone, or email with any questions you might have so far – we are always happy to help you!