Syncing multiple WooCommerce Stores to a single QuickBooks Online Company

Learn how to easily sync multiple WooCommerce stores to one single QuickBooks Online company.

Written by the MyWorks Team

Updated at July 3rd, 2023

Our WooCommerce Sync for QuickBooks Online sync allows the functionality of syncing multiple WooCommerce stores to one QuickBooks Online company. As a reminder, you'll need one active plan for each WooCommerce site you'd like to sync with QuickBooks.

There are a couple of tips that come up when configuring our sync for this type of scenario.

Connecting to QuickBooks Online

When initially activating the sync and connecting to QuickBooks Online, the process remains the same as our install instructions relate, with one change. In the Advanced Settings in your plan in your account, the value for the dropdown must be unique among all of the WooCommerce stores you wish to connect to QuickBooks Online. For example, the first site can use Connection #1, the second would then need to use any Connection number besides #1, so #2-5. And so on - until all of your stores are connected.

Order number conflicts

Now that orders from multiple sites are being synced into QuickBooks Online, there is a greater possibility for conflicting order numbers - for example: order number #545 existing on both systems, and attempting to sync to QuickBooks Online from both. In this case, the sync would error out in the second install that attempts to sync this order over to QuickBooks Online, as it already exists in QuickBooks Online under a different client - as a different order.

To mitigate this possibility of conflict, we have several best practices to choose from and adhere to:

  1. Using our WooCommerce Sequential Order Numbers Pro compatibility addon. By using this plugin combination in each WooCommerce store, you can add a store-specific prefix to each order number, which our sync will sync over to QuickBooks Online accurately. Read more here.
  2. Syncing orders over as Invoices VS Sales Receipts. If you have only two WooCommerce stores connected to QuickBooks Online, a very simple solution is to set one store to sync orders over as Invoices + Payments, and the other store to sync orders over as Sales Receipts - and they will never conflict. Read more here.
  3. Use the “Next QuickBooks #” setting when syncing orders to QuickBooks. By default, we’ll sync orders from WooCommerce into QuickBooks using the WooCommerce order ID as the Invoice/Sales Receipt number in QuickBooks. However, if it’s necessary to sync orders into QuickBooks without relying on any number from WooCommerce, we have an advanced setting that supports syncing orders into QuickBooks using the next QuickBooks invoice/sales receipt number – not relying on any WooCommerce order number. Although this results in the WooCommerce order number not matching your QuickBooks order number, this will ensure there are no order number conflicts in QuickBooks going forward.

Two-Way Sync compatibility

Normally, our sync allows complete two-way sync between WooCommerce and QuickBooks Online for data types like Products and Inventory.

When connecting two WooCommerce stores to one QuickBooks company, the only data type affected is how the automatic sync of Products from QuickBooks > WooCommerce will work.

If the product switch is enabled in Setting > Automatic Sync for the QuickBooks > WooCommerce direction, only the WooCommerce store set to Connection #1 will be able to receive new products from QuickBooks. Other connected WooCommerce stores would not have a new product synced from QuickBooks to WooCommerce when it's created in QuickBooks.

Inventory levels will still sync from QuickBooks to each connected WooCommerce store as normal if enabled in Settings > Automatic Sync. This sync happens automatically every 5 minutes.