Shopify Bookkeeping, Reconciliation and COGS

Shopify Bookkeeping and Inventory Accounting

A Shopify payout is not a day's sales. It arrives net of fees, refunds and chargebacks, often covering several days of orders, and your bank balance says nothing about what you earned. Shopify bookkeeping turns those payouts, your stock purchases and every other channel you sell through into monthly books you can run the business on.

The work covers payout reconciliation, cost of goods sold, inventory accounting and a monthly close. It doesn't include registering for and filing sales tax, which is a separate specialism, and the year-end income tax return belongs to a tax preparer, though some firms offer both. Forecasts and budgets sit with financial planning.

On shopexperts, 7 bookkeeping and accounting firms and freelancers list this service (September 2026), all with claimed profiles: 5 agencies and 2 freelancers, 6 in the United States and 1 in the United Kingdom. Compare them below and request quotes from two or three.

Test them on one real payout. Pick a Shopify Payments payout from last month and ask how they'd record it. The answer should split gross sales, discounts, refunds, fees and chargebacks, and match the payout to the orders behind it. "We book the deposit as income" is a fail.

Ask how they calculate cost of goods sold. Listen for cost per item in Shopify, freight and duty added to reach landed cost, and a stock figure at month end. A bookkeeper who expenses inventory when you buy it will show a loss in the month of a big purchase order and a windfall the month after.

Put every channel in the quote. List your online store, POS, marketplaces and wholesale invoices, with rough monthly order counts for each. Every channel settles on its own schedule with its own fees, and a quote built for one channel gets revised once the rest turn up.

Agree the close date and what you receive. "Books closed by the 15th, with a profit and loss, balance sheet and payout reconciliation" can be priced and checked. "Monthly bookkeeping" can't.

Price the backlog first. If your books are months behind, catch-up work is quoted separately from the monthly fee. Get both numbers before you sign, and agree the month the monthly service starts from.

Know the red flags. No questions about inventory. Tax advice folded into the bookkeeping fee by someone who isn't qualified to give it. A proposal that can't say who will actually do your books each month.

Payouts are net, and they lag. A Shopify Payments payout is sales minus fees, refunds and chargebacks, and one payout often spans several days of orders. Record gross sales, fees and refunds separately, then reconcile each payout to its orders. Booking the deposit as income understates sales and buries what you pay in fees.

Some money in isn't revenue. Gift cards and customer deposits are liabilities until they're redeemed or the order ships. Sales tax collected is owed to the tax authority. Both belong on the balance sheet, not in sales.

Stock is an asset until it sells. Cost of goods sold needs a cost per item on every product, and Shopify then reports gross profit and margin by product. Landed cost adds freight and duty on top. This is COGS accounting, and it's separate from running stock levels, which inventory management specialists handle.

Each channel settles differently. Online store, POS, marketplace and wholesale income arrive on their own schedules with their own fees. Each needs its own clearing account, reconciled monthly, or the differences pile up where nobody looks.

Accrual once inventory matters. Cash-basis books are fine for a small store holding little stock. Once inventory is material, accrual books match costs to the sales they produced, which is what makes a monthly margin trustworthy. Changing method can have tax consequences, so agree it with whoever prepares your return.

A fixed close date. Books closed by the same day every month give you numbers while they can still change a decision.

Frequently asked questions about ecommerce bookkeeping

How do I track Shopify COGS before I hire anyone?

Enter a cost per item on every product and check Shopify's profit reports, which are enough to spot a bestseller that earns very little. Decide early whether that cost includes freight and duty, and apply the same rule to every product, or margins across your range can't be compared. What it won't give you is a month-end stock value on a balance sheet; that's the part a bookkeeper adds.

Is inventory accounting the same as managing stock?

No. Inventory accounting puts a value on the stock you hold, moves that cost into cost of goods sold as items sell, and records write-offs for damaged or lost units. Managing stock is operational: reorder points, locations, transfers and purchase orders. Shopify's admin handles much of that side, including multi-location inventory and purchase orders. A bookkeeper uses those records; an inventory specialist designs the process behind them.

When is it time to hire an ecommerce bookkeeper?

The clearest signals are practical. You've started buying stock in volume. You've added a second channel such as wholesale or a marketplace. Your books are more than a month behind, or your first year-end return is coming up. If you're spending evenings matching payouts to orders instead of running the store, that counts too.

What access does a bookkeeper need to my store?

Their own login to your Shopify admin with access to orders, payouts and reports, never your owner account. They'll also want read-only bank and card feeds, supplier invoices, marketplace settlement reports and any wholesale invoices. Ask them to list exactly what they need in the proposal, and remove their access the day the engagement ends.

Will my bookkeeper also handle sales tax and my tax return?

Sometimes, but treat them as separate jobs. Bookkeeping records what happened. Registering for and filing sales tax is a compliance job with its own calendar, and the annual income tax return needs someone qualified to prepare it where you file. Several firms listed here offer more than one of these services. That's convenient, as long as the engagement letter lists each job with its own fee and deadline.

What happens to my books if I change bookkeeper?

Very little, if the books live in an accounting software account in your name, with the bookkeeper invited as a user. Set it up that way from day one. At handover, ask for the last reconciled month, a list of open items, and the workings behind inventory and landed cost, so the next bookkeeper starts from a known position instead of rebuilding the year.

Shopify Bookkeeping and Inventory Accounting

Cameron Lee

Freedom Finance

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What ecommerce bookkeeping services include

Payout reconciliation

Monthly close

COGS accounting

Inventory valuation

Liabilities kept out of sales

Catch-up and clean-up

Frequently asked questions about ecommerce bookkeeping

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