Shopify and QuickBooks Online Integration Guide

Set up your integration between Shopify and QuickBooks Online within minutes using our simple setup process. Below is a step-by-step walkthrough, highlighting some useful key points throughout the process.

If you have any questions, reach out to our friendly Support Team for help at any time.

1. Connect
2. Configure
3. Sync

NOTE: The QuickBooks Connector for QuickBooks Online is not compatible with QuickBooks Self-Employed, QuickBooks Desktop, and QuickBooks Enterprise.

QuickBooks users based in the USA should refer to the new app QuickBooks Commerce Accounting.

Connect

Begin by connecting your apps to QuickBooks Connector. If you haven't already connected your apps, you can follow our guides to connect Shopify and QuickBooks Online.

Configure

The configuration process below will present you with various options detailing exactly how you want your Shopify and QuickBooks Online integration to work. Please be aware that we do expect you to have some basic accounting knowledge to make sure that the integration settings are tailored to your business and accounting practices.

1. You will be required to set up your Synchronization Options before you can start configuring your workflows. You need to set up the following:

• Account Timezone
• Integrations Starting Date
• Email Sync Report Options

2. You will be presented with workflows that are all optional. In this walkthrough, these workflows will be selected to demonstrate the full capabilities of the setup process.

• Sales from Shopify will be sent to QuickBooks Online as an Invoice
• Payouts from Shopify will be sent as Deposits in QuickBooks Online
• Products from Shopify will be created in QuickBooks Online
• Stock Level Updates from QuickBooks Online will be sent to Shopify

PLEASE NOTE: At this point, integration does not sync order edits from Shopify to QuickBooks Online. 
If you edit an order in Shopify (adding line item, removing, etc.) this needs to be manually added to the corresponding invoice in QuickBooks Online. 

INVOICE CREATION WORKFLOW

When you tick the When an Order is created in Shopify, create a Sale in QuickBooks Online workflow, you will be asked to:

• Set up the filters to determine which orders will be retrieved from Shopify. You will have to set up the filters based on the Order Status
• You also have the option to select whether you want the sale to be created as a Sales Invoice or Sales Receipt to QuickBooks Online

Click on the Default Products and Advanced Options and set up the following:

• Order Number Prefix - The prefix you input here is added to all orders retrieved from your Shopify account. For example: If you have order '1234' in Shopify and you add the prefix 'SPFY' in the configuration, your order will be retrieved into QuickBooks Connector with the order number 'SPFY1234' and sent to QuickBooks Online accordingly.
• Assign Sales to Class / Assign Sales to Location - These two options allow you to choose a default Class or Location within your QuickBooks Online system. This is an option unique to QuickBooks Online, and only if you have set up Classes or Locations within your QuickBooks company file.
• Assign Sale to the - Most accounting systems require a customer record to be specified when a sales invoice is created. This particular option allows you to choose the nature of the customer record that is being created. The default option is Original Customer, however, if your Shopify customers specify a company name and you prefer to have that appear within your accounting system instead, then you can opt for the Customer's Organization option. Alternatively, if you do not want any customer records to be created within your accounting system at all you can select the Generic Online Sale Customer option, this means all sales will be synced to your Accounting system against a generic "Shopify" customer record that you will create or leave blank to use the default Generic customer.
• Automatic Invoice Numbers - This option allows you to disregard the Shopify order number completely, and use the sequential numbering convention within your accounting system.
• Discount Product - You can specify a dedicated discount 'Item' so you can track your discounts on sales.
• Rounding Off Product - Select the preferred product to be used when sending rounding discrepancies as a line item.
• Use Shipping Item - You may be charging your customers extra shipping charges on your sales. If this occurs, the integration can allow you to specify a dedicated "Item" to assign these shipping charges. This will allow you to easily track any revenue generated from shipping charges.
• DueDate Offset - A due date type will be assigned if transactions do not have a due date. This is calculated using the transaction date, the Due Date Offset and the type specified. If not set, the transaction date is used as the due date.
• Allow Credit Card Payments - Tick this option if you want to allow credit card payments for the transactions.

• Next, you'll be taken to the tax configuration page. Here, for each tax created/defined in your Shopify, you must select its corresponding tax code in QuickBooks Online. You can read more about the tax configuration here.

• You can also select how you want to match your Shopify products with your QuickBooks Online products. You can either match by Name or SKU. In order for sales to properly integrate with your accounting system, we expect that you have all of your Shopify items set up with unique SKUs. 

PLEASE NOTE: With QuickBooks Online integrations, we have 2 product matching options:
NAME: We match the product's SKU field from Shopify to the product's NAME field in QuickBooks Online
SKU: We match the product's SKU field from Shopify  to the product's SKU field in QuickBooks Online

• Additionally, if you want the new items within your invoices from Shopify to be created in QuickBooks Online, just simply tick the box before the Create New Items in QuickBooks Online setting. In this section, you'll have to select the income and expense accounts to be used for your inventoried and non-inventoried items. You can find more information on the integration of items here.

PLEASE NOTE: QuickBooks Connector can only assign the COGS account for the products upon creation BUT we will not sync the COGS price of products.

• Then, the Send Payments from Shopify to Quickbooks Online settings will allow you to select whether you want payment data from Shopify to be registered against your sales within Quickbooks Online.

• If you want to map different payment methods to different clearing accounts, this can be done by clicking the Advanced Options link:

• You also have the option to Create Credit Notes in QuickBooks Online. In this workflow, you will be asked to map a Fallback account from which the payment money is refunded. You will also be asked to input your preferred Refund Number Prefix which will be appended before the refund receipt number.

PLEASE NOTE: Select the Refunded and Partially Refunded status on the Order filter if you wish to sync credit notes to your accounting app.

• Within the integration, you can opt to sync Shopify Fees that will be as Expenses under Bills in QuickBooks Online.

PLEASE NOTE: To sync Fees in QuickBooks Online, the Payments section the Payment Method accounts should be configured according to the following:

• QuickBooks US and CA: Credit Cards or Checking Bank accounts.
• QuickBooks AU and UK: Cash accounts.
• Other regions: Configure any account.

• Do not forget to click the Save button to keep your progress.

PAYOUTS SYNC WORKFLOW

By enabling the Payouts Workflow, you are allowing QuickBooks Connector to automatically create Deposits within QuickBooks Online for the Payouts sent to your account by Shopify.

If you are unsure as to what exactly Shopify Payouts are, please refer to this Shopify support guide:
https://help.shopify.com/en/manual/payments/shopify-payments/getting-paid-with-shopify-payments

PLEASE NOTE: If you wish to enable Payouts to sync to QuickBooks Online, we recommend that you disable the Orders workflow above, which could double up your reported revenue if not set up correctly.

• You will be asked to map the Into Bank Account field. This is where we will record your Shopify Payouts as a Bank Transaction. The account to be used must be an "Other Current Asset" or a "Bank" account. The selected account will be the Chart of Account that you will select when viewing your Deposit on your QuickBooks Online account.
• To view the Deposits created in QuickBooks Online:

  Accounting > Chart of Accounts > Select Account Assigned to the Into Bank Account field

• In the Create a Deposit section, you will be asked to map the Default Payment Method. Assign a payment method here, this method will be used if the payment method from Shopify is missing in the payouts. 

Use Income Accounts Section:
The income account to be selected here is where you will be able to map the different Payment Methods to specific clearing accounts. We will send the Payment Methods that do not have an assigned Income Account to the set Default Account.

Use Expense Accounts Section:
The expense account to be selected here is where we will map the Fees, Charges, and Taxes part of the Payout.

• Do not forget to click the Save button to keep your progress.

PRODUCT CREATION WORKFLOW

If you want all your new products from Shopify to be created in QuickBooks Online, all you have to do is to tick the When a Product is created on Shopify, create new Items in QuickBooks Online workflow. You'll have to select the income and expense accounts to be used for your inventoried and non-inventoried items. You can find more information on the integration of items here.

PLEASE NOTE: QuickBooks Connector can only assign the COGS account for the products upon creation BUT we will not sync the COGS price of products.

• Do not forget to click the Save button to keep your progress.

STOCK UPDATE WORKFLOW

When you tick the When Stock Levels are updated in QuickBooks Online, update stock levels in Shopify workflow, you will be asked to select how you want to match the items to QuickBooks Online items either by Name or SKU and the Store Location where the stock should be updated.

PLEASE NOTE: This option should only be enabled if you have stock levels set up in QuickBooks Online prior to the integration. Otherwise, you will risk wiping out your Shopify stock levels. Click here to know more about our Stock Control process.

• Do not forget to click the Save button to keep your progress.

Sync

Voila! Your account is now ready to sync your data across your apps! When your auto-sync is on, your account should sync every hour but you can trigger manual sync anytime! Just click the Sync Now button on the Synchronization Options on top of your Manage tab!