What to do when Shopify and Square don’t sync with QBO

What to do when Shopify and Square don’t sync with QBO

I'm often asked about issues with Shopify and Square integrations, particularly when they don't sync correctly with QuickBooks Online (QBO). While these integrations are great when they work, discrepancies can arise.

One of the most common questions I receive is, "Why are my Shopify/Square sales different from what QBO shows?" There are several reasons for this. Sometimes, an integration may simply stop syncing, requiring manual entry of missing sales.

However, the most frequent reason relates to how Shopify and Square record sales versus how your QBO is set up (e.g., accrual vs. cash basis). Shopify Payouts and Square Transfers are what you should reconcile against your QBO file. Both platforms typically create an asset account to hold these funds. I usually prefer to set up a bank account for these holding funds to simplify reconciliation against payouts.

Both platforms will sync each transaction or daily summary to a Sales Order or Sales Receipt in QBO, which can be difficult to find and is not editable. These Sales Orders will post to the aforementioned holding account. Additionally, both platforms deduct their selling fees from each transaction before depositing the balance into your bank account.

The key is to reconcile the sales, less fees, against the Payouts/Transfers. The holding account, whether an asset account or a bank account on your books, should always balance to zero. This reconciliation should be performed monthly to prevent extensive cleanup efforts and inaccurate numbers.

Another common anomaly with Shopify involves how payouts are structured. Payouts generally take 2-3 days to reach your account. Sales from a Friday, Saturday, and Sunday might not be paid out until the following Tuesday. If the month ends on that weekend, sales from the 30th, 31st, and 1st could be combined, often leading to discrepancies between QBO and Shopify/Square sales totals.

In conclusion, you may not always get the sales totals to match if you are using the sync features from Shopify and Square but als long as you are reconciling the Payouts and accounting for Sales less fees you should be good!