A store can look healthy in its dashboard and still be wrong in its books. Sales are recorded when orders happen, money arrives days later in batches net of fees, refunds reduce it, disputes freeze some of it and ad spend sits on someone else’s statement. If nobody reconciles the pieces each month, small differences become large unexplained ones by year end.
This checklist is the routine we recommend for small and mid-sized online stores. It is general information rather than accounting advice, and your accountant may want things done differently. For a deeper look at the payout problem, see why the Shopify payout never matches sales and our Shopify and QuickBooks guide.
Set the rhythm
Close the month on a fixed working day, such as the fifth, so that data is complete and comparable. Use the same checklist each time and keep the evidence: exports, screenshots and notes. A consistent routine takes less time than an occasional heroic catch-up and makes your accountant’s work cheaper.
The twelve checks
| # | Check | What to compare | What a difference usually means |
|---|---|---|---|
| 1 | Payout reconciliation | Each processor payout against the orders, fees and refunds it covers | Timing, fees, refunds, reserves or missing orders |
| 2 | Sales by channel | Platform sales reports against ledger revenue by channel | Unposted orders, mapping errors or duplicates |
| 3 | Refunds and returns | Refunds issued against refunds recorded | Partial refunds, refunds on prior-month sales |
| 4 | Fees | Processor, marketplace and app fees against statements | Unrecorded fees or fee rate changes |
| 5 | Disputes and chargebacks | Open disputes, won and lost amounts, dispute fees | Funds held, fees not recorded |
| 6 | Sales tax | Tax collected by jurisdiction against the liability account | Wrong codes, refunds, manual orders |
| 7 | Shipping income and cost | Shipping charged against carrier invoices | Under- or over-charging |
| 8 | Inventory and cost of goods | Stock value and cost of goods sold against purchases and counts | Shrinkage, wrong costs, unrecorded receipts |
| 9 | Ad spend | Platform spend against card or bank charges | Missing invoices, currency differences |
| 10 | Gift cards and store credit | Liability balance against issued and redeemed | Unrecorded redemptions |
| 11 | Bank and card feeds | Uncategorised transactions | Missing receipts or unknown charges |
| 12 | Month-end report | Revenue, margin, cash, tax and open items | The summary that ties it together |
1. Payouts
A payout is a lump sum: orders, minus fees, minus refunds, minus disputes, plus or minus adjustments and reserves. Reconcile each payout by listing the transactions that make it up and checking that they total the deposit. Software can do this matching for most payouts, leaving a short list of exceptions to review. Without a record of the payout composition, you can only guess at the cause of a difference. Our payout reconciliation and bookkeeping service automates this step.
2 to 4. Sales, refunds and fees
Compare the revenue the platform reports for the month with revenue in the ledger, by channel. Differences often come from orders created or edited late, from currency conversion and from the date used, for example order date versus payment date. Pick one convention and keep to it. For refunds, check that each one is recorded and matched to the original sale, including refunds on previous months’ orders. For fees, compare the processor and marketplace statements with what you have recorded. A small change in a fee rate across thousands of orders is easy to miss.
5. Disputes
Disputed funds are often held until the case resolves. Track the open cases, the amounts held, the dispute fees and the outcomes. If you win, funds return; if you lose, the amount and fee become expenses. Keep the evidence for each, as described in Stripe dispute evidence, and review the process using chargeback prevention.
6. Sales tax
Compare tax collected, by place, with the balance in your liability account, and check refunds reversed the correct amounts. Check the monthly sales by place against any thresholds. Our sales tax automation guide explains the underlying questions, and your accountant decides the filing details.
7 to 9. Shipping, inventory and ads
- Shipping. Compare what customers paid for shipping with what carriers charged. A persistent gap is margin leaking, and it usually points to a pricing rule that needs adjusting.
- Inventory. Reconcile the value of stock on hand with purchases, sales and counts. If you use periodic counts, compare the count to the system and book the adjustment. Wrong unit costs distort margin on every sale.
- Advertising. Match platform spend with card statements. Currency and timing differences are normal, but missing invoices are not.
10 and 11. Gift cards, credits and the bank feed
Gift cards and store credits are liabilities until redeemed. Check issued and redeemed balances against the platform. Then clear the bank and card feed so that every transaction is categorised and there is a receipt or an explanation for anything unusual. Uncategorised items are small today and a headache at year end.
12. The month-end report
End with a one-page summary: revenue by channel, gross margin, fees as a percentage of sales, refund rate, ad spend and return on it, cash position, sales tax liability, open disputes and unresolved reconciling items. The act of writing it often reveals what the individual checks missed. Our sales reporting and weekly digest work builds this automatically.
Multiple currencies and channels
Stores that sell in several currencies or through several marketplaces add steps. Record the currency of each sale and the exchange rate used by the processor, and decide how you book conversion differences. Keep each marketplace’s settlement report, since it shows fees, advertising charges, refunds and reserves that do not appear in the store platform. Tag every ledger line with its channel so that the margin report can compare them. Without that, the best-looking channel is often the one whose costs are least visible.
Prepare for year end during the year
The monthly routine makes year end a summary rather than a project. Save the monthly reports, keep documents for unusual transactions, and note decisions such as how you treat marketplace advertising or inventory write-downs. Ask your accountant what they need: a list of reconciled accounts, inventory counts at year end, sales tax filings and a schedule of fixed assets. Handing over a reconciled file with notes is the quickest way to reduce an accountant’s bill.
| Item | Keep |
|---|---|
| Reconciled payouts | Monthly exports and the matching file |
| Inventory counts | Count sheets and adjustments with reasons |
| Tax filings | Returns, confirmation numbers and payments |
| Dispute records | Evidence submitted and outcomes |
| Decisions log | Conventions chosen and why |
What automation prepares
| Task | Automation can | A person still |
|---|---|---|
| Pull data | Fetch payouts, orders, fees and statements on schedule | Decides the cut-off and conventions |
| Match | Match payouts to transactions and flag differences | Investigates unexplained items |
| Categorise | Apply rules to bank and card lines | Reviews unusual transactions |
| Post | Create journal entries from summarised data | Approves before posting |
| Report | Build the monthly summary | Reads it and decides what to do |
| Alert | Warn about large differences or rate changes | Takes action |
When to bring in your accountant
Automation prepares the books, but an accountant gives them meaning. Agree early how often you will meet, what you will send beforehand and which questions to raise. Typical topics include how to treat marketplace fees, advertising credits, gift cards and inventory write-downs, whether to change your accounting method as you grow, and how to prepare for tax deadlines. Share the monthly report and the list of unresolved items before each meeting, so the time is spent on decisions. Ask the accountant to review your reconciliation routine once a year and suggest improvements. A short, regular conversation is cheaper than an annual rescue, and it keeps your numbers reliable enough to base real decisions on.
A worked example
A store with 1,100 orders a month spends about 9 hours on bookkeeping at $25 an hour, or $225. The owner mostly exports spreadsheets and matches rows by eye. With an automated pull and match, exceptions drop to about 40 lines, taking 2 hours to review, plus 1 hour for the report. The monthly time falls to 3 hours, saving about 6 hours and $150 a month, and the accountant’s year-end clean-up shrinks. More importantly, a fee-rate change that would have gone unnoticed is flagged in the month it happens, saving an estimated $90 a month for the rest of the year. The figures are illustrative.
Mistakes to avoid
- Booking payouts as sales, hiding fees, refunds and reserves.
- Changing conventions mid-year, such as order date versus payment date.
- Ignoring small unreconciled items, which grow.
- Mixing personal and business transactions.
- Leaving inventory costs out of date.
- Treating the report as optional. It is the control that proves the checks happened.
Sources and further reading
Figures and rules in this guide come from the primary pages below. Platform limits and prices change, so open the page before you build on a number.
- Shopify Help Center: payouts, how Shopify payments payouts are composed
- Stripe Docs: payout reconciliation, matching payouts to transactions
- IRS: Small business and self-employed tax center, recordkeeping guidance for US small businesses