What to know before you start
Shopify's point of sale, Shopify POS, isn't a separate system. A sale made in store is a Shopify order, just like a sale made on the online store. That's what makes the link with the books possible: there's a single source to connect.
On the other side, there are two QuickBooks. QuickBooks Online connects through an app from the Shopify App Store. Intuit, the maker of QuickBooks, publishes one, and other publishers offer their own. QuickBooks Desktop goes through a different connector, with its own limits. Everything that follows is about QuickBooks Online.
A connector does only one thing: it reads what happened in Shopify and writes it into QuickBooks. It doesn't decide for you where each amount should go. That's where the work is.
The steps, in order
Choose how sales are recorded
There are two ways to do it. Either each sale becomes an entry in QuickBooks. Or the connector writes a summary, per day or per payout: so much in sales, so much in taxes, so much in fees.
A store that makes fifty small sales a day doesn't need fifty entries. The summary keeps the books readable, and it matches the deposit you see arrive at the bank. One entry per sale is useful when you want to find a specific order in QuickBooks.
Map each thing to its account
The connector asks where to put sales, discounts, refunds, shipping charges, card processing fees, gift cards and store credits. Your accountant already has a chart of accounts. We start from theirs; we don't invent a new one.
Set up GST and QST
Shopify calculates two taxes, on two lines. QuickBooks has to receive them separately, each with the right tax code, otherwise the end-of-period return won't balance. We check it with a real sale, then with a real refund.
Reconcile the deposits
Card sales reach the bank as payouts: a single deposit for several sales, fees already taken off. The connector has to record the payout and its fees so that the amount in QuickBooks is the one on the bank statement.
Cash doesn't go through any payout. It stays in the drawer until the bank deposit. It needs its own account in QuickBooks, otherwise cash sales float somewhere between the till and the bank.
Test on a real day
Before trusting the link, we run a full day: a card sale, a cash sale, a refund, a credit issued, a credit used. Then we compare Shopify's sales report with what went into QuickBooks. The two totals have to be identical.
The pitfalls
- Store credits and gift cards. A credit issued isn't revenue. It's a debt to the customer until the day she uses it. Set up wrong, the connector counts the sale twice: when the credit is issued, then when it's spent.
- The start date. The connector imports from a given date. If your accountant has already entered the month's sales, you'll get duplicates. We pick the start of a period, with them.
- Refunds and exchanges. An exchange at the till is a return and a sale in the same transaction. We check that both halves come through.
- Inventory. Shopify already keeps the inventory. Nothing requires copying every item into QuickBooks. For a business whose items change every day, it's actually best avoided.
What we did at Bon Flow
Bon Flow sells second-hand women's clothing and accessories in store, in Saguenay. Customers drop off clothes they no longer wear in exchange for store credit. Several employees at the till, an inventory that changes every day, credits issued and used to track, and books that have to keep up with all of it.
We built the website, which explains the concept and how drop-offs work. We set up Shopify POS for a team, with one login per employee. Consignment credits are handled as store credits that add up and can be used in part: they live in the point of sale, not in a notebook on the side.
Then we set up the connector between Shopify and QuickBooks so that sales, credits and deposits land cleanly in the books. In March 2026, the store was running on this point of sale.
When it's not the right solution
If you make a few sales a week, a connector to keep an eye on isn't worth it. Shopify's monthly report, handed to your accountant, does the job.
If you're on QuickBooks Desktop, the path is different. Before connecting anything, ask whether it's time to move to QuickBooks Online.
If you don't have accounting software yet, the question is a different one. We connect a Shopify store to QuickBooks or to Zoho Books: the choice depends on the rest of your tools. That's the subject of our page Websites and e-commerce.