Shopify QuickBooks Online Integration: How to Connect Two Platforms via Synder

Shopify QuickBooks Online Integration: How to Connect Your Platforms via Synder

Every specialist working in the ecommerce sphere will tell you that efficient operations are the cornerstone of success. Sellers, their accountants and bookkeepers are always on the lookout for tools that streamline processes, from inventory management to financial record-keeping. 

The QuickBooks and Shopify integration is a solution designed to seamlessly synchronize financial data between Shopify stores and QuickBooks Online accounts. Whether you make a sale, issue a refund, or add new products to your store, with Synder, these changes are automatically reflected in your QuickBooks Online account. This real-time synchronization eliminates manual data entry, ensures accurate financial reporting, and enables businesses to focus on growth rather than administrative tasks.

This article will delve deep into the QuickBooks and Shopify integration via Synder, highlighting its benefits and features.


1. Synder benefits: Reasons to implement Shopify QuickBooks Online integration

2. How to set up the QuickBooks Shopify integration via Synder

3. Key features of the QuickBooks Shopify integration via Synder

4. Shopify QuickBooks integration FAQ

Synder benefits: Reasons to implement Shopify QuickBooks Online integration

The benefits of Shopify QuickBooks Online connection are limitless. If you’re looking for new and more efficient ways to connect Shopify to QuickBooks online, here are some Synder advantages you might be interested in.

Connection of more than one sales channel and/or payment platform

When integrating sales channels to accounting software such as QuickBooks, it’s important to record all the financial details to get insightful and accurately prepared reports. If you have payment gateways in use besides Shopify Payments, Synder provides an option of connecting additional platforms so that you can store the transactions with the information taken from both ends, Shopify and the payment platform. The data will be recorded accurately without duplicates or entry errors. 

Synder also supports the connection of additional ecommerce stores so that business owners can track their sales across all platforms. 

Per Transaction and Daily Summary data sync options

While the Per Transaction sync seems clear, Daily Summary might be confusing. This is an automated option to gather all sales, fees, refunds, taxes, and discounts for the day and post them as a single record per connected platform to your books. If you connect an additional payment platform, let’s say PayPal, each day you’ll get 2 journal entries reflecting the records from Shopify Payments and PayPal. 

Note: No customer/product data is transferred to your QuickBooks when choosing the Daily Summary sync. 

Secure data transfer

When sales or transactional data is recorded, the integration ensures that all financial data is transferred securely between platforms, adhering to the highest standards of data protection. Synder is SOC 2 Type 2 Certified and provides the highest level of security and compliance. 

Enhanced reporting

By recording all the financial data provided by the connected platforms, you’ll be able to generate the most detailed and accurate P&L and Balance Sheet reports, that will cover all the income and expense details from Shopify and additional payment gateway(s) if connected. 

How to set up the QuickBooks Shopify integration via Synder

Connect your Shopify account to QuickBooks Online via Synder by following the steps below – create a free account (no card details required). 

1. Create an account

First things first, you need to choose the product you want to utilize. Synder provides you with two options: Synder Sync and Synder Insights. 

Synder onboarding (Shopify + QBO)

Synder Sync is an actual connector between your sales channels and QuickBooks Online, while Synder Insights is an analytical tool that allows you to track the most important metrics of your ecommerce business. 

You can choose either one or both products. 

2. Set up the organization

Fill out the necessary organization information, such as the name of the organization, time zone, country, industry and how long the business has been on the market. 

Synder onboarding (Shopify + QBO)

3. Select your platform (Shopify)

Choose Shopify for the sales integration.

If the Shopify store in question accepts payments via payment gateways other than Shopify Payments, it’s strongly recommended to connect these payment platforms to Synder as well. By doing so, you’ll get flawless records of sales, fees, refunds, and payouts from the connected payment gateway with additional data provided by Shopify orders.

Synder onboarding (Shopify + QBO)

Note: Click ‘View all integrations’ to see all the platforms available for integration. 

4. Select accounting software (QuickBooks Online)

Choose QuickBooks Online among the provided options. 

Synder onboarding (Shopify + QBO)

Synder is also available for integrations with QuickBooks Desktop, Xero and its own accounting software – Synder Books. 

5. Choose the sync mode

As was said above, Synder provides two options for transaction synchronization: per transaction or on a daily basis. Choose the one that suits you best.

Synder onboarding (Shopify + QBO)

Don’t know which one to choose? Check out our guide to learn more about the workflow and benefits of both modes.

6. Connect platforms

At this step, you’ll need to connect your QuickBooks and Shopify accounts. It’s really easy, just remember that for Shopify, you’ll need to install Synder as an App in your actual Shopify account. 

Synder onboarding (Shopify + QBO)

When both accounts are connected, Synder will finalize the process and synchronize the most recent transactions to your books. 

And you’re good to go! Now your Synder account is ready to sync. Keep in mind that you need to customize the Synder account to your needs so make sure all the important accounting and bookkeeping options are enabled in the settings.

If you already have a Synder account and want to add Shopify, check out Synder’s guide on how to connect Shopify to an already existing account.

Have questions about the onboarding process? Don’t know what to choose at a particular step? Get all your questions answered at a live webinar! Attending our weekly webinar where Synder specialists show how to set up your account and how Synder can help you automate manual bookkeeping tasks – reserve your spot

Key features of the QuickBooks Shopify integration via Synder

Instant synchronization and historical data import

Synchronize the data between the Shopify and QuickBooks accounts in real-time and get the records of order details such as the product name, quantity, total cost, shipping cost, tax, and customer information. Get the data recorded either on a per transaction or daily basis. You can also import the historical data from your Shopify account directly into QuickBooks to see the whole picture of your business performance across time. 

To store additional financial data from the transaction that went through a platform other than Shopify Payments, you’ll have to connect the payment platform in use so that Synder is able to recognize all transactions and store them successfully. 

Error-free multi-channel reconciliation

Ease your reconciliation process with the real bank account by pre-checking all the transactions recorded in QuickBooks from the platforms you’ve connected to Synder. When Synder records a payout from a payment platform, it’s automatically reflected in your QuickBooks Online account (‘Bank feeds’ tab). By matching the stored transactions, you’ll be able to decrease the discrepancy and get a zero difference between the two balances during the actual reconciliation process. 

Payouts won’t duplicate your bank feed records.

Inventory and COGS tracking

Once you have inventory and COGS tracking set up in Synder, the software will be able to categorize the income by the product income accounts specified in your books. This means that if products have the same names or SKUs across all the connected platforms, Synder will recognize these products during synchronization and match them automatically. 

For Shopify, Synder will automatically create new products in your QuickBooks account with the same item names, SKUs, sales prices and casts taken from the Shopify account after the transaction containing this data is synced to your books. 

Note: Quantities on hand won’t be transferred to the accounting company, you’ll need to enter them manually into your QuickBooks Online account. 

Automated categorization

All you need to do to set the automated categorization rules for assigning products, classes and locations, sending automatic reminders, and filling out missing data is to create your own rules. Once created and enabled, Synder will apply them automatically when the new transactions are recorded. To set a rule, you have to choose a trigger that’ll activate the action. Or you can take one of the pre-designed Synder templates and just edit it a bit so it suits your needs. 

So how does this feature work in practice? Let’s say, you’re selling from Canada and have issues with recording your taxes. In this case, if the shipping address in the Sales Receipt from Shopify includes “Ontario”, then Synder will apply the appropriate state tax in QuickBooks Online. Without Synder, QuickBooks Online might recognize it as another state with the same tax rate.

Check out a use case about Canadian taxes – learn more about how Synder handles this problem in QuickBooks Online.

Multicurrency management

Depending on your settings, Synder will create records based on the original currency of the transaction in your QuickBooks account and convert them to your home currency according to the exchange rate provided by Shopify or another payment platform through which the transaction was made, recording them directly in your QuickBooks multicurrency wallet. 

Sync rollback

If, for any reason, you’re not satisfied with the sync results in your QuickBooks Online account, use Synder’s rollback feature to undo all unwanted changes, without causing any damage to your accounting data. After the synced data from Shopify is deleted, you can adjust the configurations, apply the automated categorization and then resync the accurate data into your books. You can choose how you’d like to rollback: per transaction or in bulk.

Note: Rollback doesn’t reinstate the number of syncs available. 

Wrapping up

Shopify and QuickBooks offer businesses a comprehensive solution when integrated. By merging the capabilities of both platforms, businesses can enjoy streamlined financial processes, reduced errors, and a clear picture of their financial health. This Shopify and QuickBooks integration via Synder not only saves precious time for businesses but also ensures accuracy in accounting and financial reporting.

Shopify QuickBooks integration FAQ

To which QuickBooks Online account Synder records the financial data from Shopify?

The tool records the financial data to your Shopify account. When the first transaction is synced, Synder automatically creates a Shopify clearing account in your Chart of Accounts, where all future Shopify transactions will be stored. Once the money payout takes place, Synder will transfer it to your checking account. 

How to sync Shopify Manual Orders and Manual Order refunds?

You’ll need to have additional settings for Manual Orders and Manual Order refunds created in Synder. 

Go to Settings → click on the Configure button under Shopify → click on Manual Order/Manual Order refund tab → Sales → select the account manual orders will be deposited to or just leave the default Shopify Manual Order (required for Synder) → Update.

For a detailed step-by-step guide, follow the link – Setup for synchronizing Shopify Manual Orders and Manual Order refunds.

Note: Without the Manual Order and Manual Order refund settings enabled, Synder won’t be able to process manually created orders and refunds, they’ll be skipped. 

How to sync Shopify POS orders and refunds?

Just like with Manual Orders and Manual Order refunds, Shopify POS merchants will need to create additional settings for Shopify POS Orders. The steps are also similar to the previous case.

Go to Settings → click on the Configure button under Shopify → click on POS Order/POS Order refund tab → select the account POS orders will be deposited to or just leave the default Shopify POS Order (required for Synder) → Update.

For a detailed step-by-step guide, follow the link – Setup for synchronizing Shopify POS Orders and POS Order refunds.

Note: Without the POS Order and POS Order refund settings enabled, Synder won’t be able to process manually created orders and refunds, they’ll be skipped. 

Is it possible to track the same product that has different names across platforms?

Yes. To do this, you’ll need to set up product mapping for the system to know which products are to be treated and tracked as one. You can also handle it with the help of the Automated Categorization feature and Rules. 

Learn more about the product mapping feature and how it works – Synder Product Mapping: A Short Feature Overview.

Is it possible to get an instant low-stock alert?

Synder can do that. To enable this action, you’ll need to utilize the Automated Categorization feature. The rule you’ll create will monitor the quantity on hand for your products in the QuickBooks Online account and notify you via email once the levels are below your specified inventory threshold. 

Two options are available:

Option 1

Go to Categorization RulesRulesCreate Rule → (choosing the trigger) Sales Receipt: Created → (choosing the condition) IF: Line Product or Serviceless (enter the amount you need) → Yes → (choosing the action) THEN: Email Inventory for [product name] went down → [Product name] went down. Please, repurchase.

This will tell Synder that an email should be sent to the company owner with any text you specify in your condition.

Note: The Rule will be activated once a sales receipt is created. 

Option 2

You can use a Synder template and edit it so it suits your needs. 

Go to Categorization RulesTemplatesInventoryAlert inventory goes down in Sales ReceiptTry it out. 

Check out a detailed Synder guide to learn more – How To Get Instant Low Stock Alerts.

Can I add more platforms to Synder?

Yes. In addition to a Shopify account, you can also connect to Synder other ecommerce platforms, such as eBay, Amazon, Etsy, etc. Keep in mind that it’s recommended to connect both ecommerce platforms and payment gateways so Synder is able to recognize all transactions and record them into your QuickBooks Online account. 

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