Shopify Accounting Software and Bookkeeping Guide

Shopify records your orders and pays out your sales, but it does not keep your books. Shopify accounting means turning orders, payouts, fees, refunds, sales tax and stock into a ledger that matches your bank account. For that you need three things: accounting software, a reliable way to bring Shopify payouts into it, and a monthly routine that checks the two agree.

Does Shopify do accounting?

No. Shopify's finance reports show gross sales, discounts, returns, taxes and payouts, which are useful source data. They are not a general ledger. Shopify does not reconcile your bank account, record supplier bills, track what you owe or produce a balance sheet. Your Shopify plan fee, app subscriptions, ad spend and stock purchases also sit outside its sales reports.

That is why every Shopify store eventually connects an accounting system. The decision is which one, and how payout data reaches it.

How a Shopify payout becomes accounting entries

A Shopify Payments deposit is a net figure. It combines several kinds of money, and each belongs in a different account. Recording the deposit as sales overstates revenue and hides your fees.

Here is one week of Shopify Payments activity for a store:

The clearing account is what keeps this tidy. Each payout is recorded into it line by line, and the bank deposit clears it out. When the clearing account sits at zero after a payout, every part of that deposit has been explained. A balance left behind points to a missing refund, fee, chargeback or deposit.

A payout often includes orders from the previous few days, so a payout that lands on 2 November can contain October sales. Splitting the payout by order date keeps each month's revenue in the right month.

What a Shopify store records besides payouts

Payouts cover card sales through Shopify Payments. The books also need everything else that moves money:

• Other payment methods. PayPal, Amazon Pay and other gateways pay out separately. Record each from its own statement through its own clearing account.
• Shopify bills. Your plan, app charges and Shopify Shipping labels arrive on a separate Shopify bill. Record them as expenses when they are charged.
• Cost of goods sold. The cost of each unit sold, including the freight and duty to get it to you. See our inventory accounting guide and landed cost guide.
• Stock purchases. Supplier invoices for stock add to inventory, an asset, until the units sell.
• Gift cards. A gift card sale is money you owe the customer in products. It becomes revenue when the card is redeemed.
• Chargebacks. A disputed order and its fee come out of a later payout. Record both, and the reversal if you win.
• Ad spend and other operating costs. Meta, Google and TikTok charges, contractors, software and warehouse costs.

Shopify accounting software: the main setups

There are three common ways to set up accounting for a Shopify store. Each one needs a general ledger. They differ in how payout data reaches it and who does the monthly work.

QuickBooks or Xero with a payout connector

QuickBooks Online and Xero are general accounting products with large networks of accountants who already know them. Neither splits a Shopify payout into its parts on its own, so most stores add a connector. A2X, Link My Books and Synder read Shopify settlements and post summarised entries to QuickBooks or Xero.

This setup suits a store whose accountant already works in QuickBooks or Xero. The trade-off is two subscriptions, a mapping to maintain between them, and connector pricing that usually rises as your order volume grows.

An ecommerce bookkeeping service

Services such as Finaloop combine ecommerce accounting software with bookkeeping work done for you. They suit owners who want the monthly work handed off. Expect a higher monthly cost, and check how pricing changes as revenue grows and what is included at each level.

An ecommerce ledger with payout matching built in

Nummbas-FO can record routine transactions within the limits you set and prepare month end for your review. You can do the bookkeeping yourself or invite your accountant to work in the same books. If your accountant prefers QuickBooks Online or Xero, Nummbas can instead send each payout to them as a summary.

What each setup costs

Prices are US list prices with monthly billing as of November 2026, before introductory discounts. A connector is paid on top of QuickBooks or Xero, so QuickBooks Plus with an A2X plan that includes cost of goods sold comes to about $190 a month at 500 orders.

A monthly Shopify bookkeeping routine

Bookkeeping is easier as a short weekly habit plus a month-end close than as a quarterly catch-up.

Every week

1. Match each Shopify Payments payout to its bank deposit and check the clearing account returns to zero.
2. Record supplier bills and attach receipts for anything paid by card.
3. Review any bank line that is still uncategorised.

At month end

1. Reconcile every bank account, card and payment gateway to its statement.
2. Split any payout that spans two months so each month carries its own sales.
3. Record cost of goods sold for the units sold and check your inventory value.
4. Check sales tax payable against what you collected and what Shopify remitted for you.
5. Review the profit and loss statement for anything unusual, such as a refund spike or a missing ad bill.
6. Close the month so earlier figures cannot change without anyone noticing.

When to hire a Shopify bookkeeper or accountant

Plenty of owners keep their own books in the early years. Bring in help when one of these is true:

• You sell in several US states or countries and are not sure where you owe sales tax, VAT or GST.
• You carry significant inventory and need accurate cost of goods sold for your tax return.
• Payouts no longer match deposits and you cannot find why.
• You are raising money, applying for a loan or preparing to sell the business.
• The monthly close takes you more than a day.

Shopify accounting FAQs

Does Shopify have built-in accounting software?

No. Shopify provides sales, payout and tax reports, which are source data for your books. You still need accounting software to reconcile bank accounts, record bills and inventory, and produce a profit and loss statement and balance sheet.

What is the best accounting software for a Shopify store?

It depends on how you work. QuickBooks Online or Xero with a connector such as A2X suits a store whose accountant already uses them. A bookkeeping service suits owners who want the work done for them. Nummbas Books suits owners who want payout matching, bookkeeping and inventory costing in one product at a price that does not rise with order volume.

How do I record Shopify payouts in my books?

Record each payout through a clearing account. Enter the gross sales, discounts, shipping income, sales tax, refunds and fees from the payout report, then match the net deposit from your bank. The clearing account should return to zero once the deposit is matched.

Should Shopify sales tax be recorded as income?

No. Sales tax you collect is money you owe to the tax authority, so record it as a liability until you pay it. Tax that Shopify collects and remits for you, such as on Shop channel orders in the United States, never reaches your account and should not be recorded as your income or liability.

Can I do Shopify bookkeeping myself?

Yes, if you keep a weekly routine and your sales are in one or two tax jurisdictions. Software that splits payouts and suggests categories removes most of the data entry. Bring in a bookkeeper or accountant as your inventory, sales tax obligations or reporting needs grow.