How Do You Fix Ecommerce Books That Are a Year Behind?

Why ecommerce books fall behind faster

Every business can get behind. Ecommerce gets behind badly, because the raw data is wrong in a way that ordinary bookkeeping does not reveal.

A Shopify or Amazon payout is not revenue. It is gross sales minus platform fees, minus refunds, minus advertising, sometimes minus a loan repayment, with sales tax somewhere in the mix, netted into a single deposit. Book the deposit as income and the revenue is understated, the fees are invisible, the margin is fiction, and the sales tax that belongs to a state is sitting in your profit. A year of that is not a set of books that needs tidying. It is a set of books that has to be rebuilt.

Add inventory, and a second problem appears. Without cost of goods sold recorded properly, the profit and loss shows a healthy number in months when you bought nothing and a loss in months when you restocked.

What a cleanup costs

Published market benchmarks for 2026 put ecommerce cleanup in a wide band, because the work scales with the number of channels, the transaction volume and how badly the data was recorded in the first place.

The order the work has to happen in

Cleanup done out of order gets redone. This is the sequence that holds:

• Fix the chart of accounts first, so sales, platform fees, merchant fees, shipping income, shipping cost, refunds and sales tax each have a home.
• Set an opening balance date: the last month end where the balance sheet was genuinely right, or the start of the backlog if there is no such month.
• Connect every account and gateway, including the second processor everyone forgets, and pull full-year statements rather than feeds, which usually reach back only 90 days.
• Re-record payouts from settlement reports, month by month, splitting each into gross sales, fees, refunds, shipping and sales tax.
• Reconcile every bank and card account to the statement, every month, with no unreconciled difference carried forward.
• Book inventory and cost of goods sold from purchase records and counts, so gross margin means something.
• Move collected sales tax into a liability account and compare it with what was actually filed and paid.
• Close each month and produce the profit and loss and balance sheet before moving to the next.

What you need to have ready

The single biggest cause of a cleanup running long is missing documents, so gather these before the work starts: full-year bank and credit card statements for every account, platform settlement or payout reports for each channel and each month, merchant processor statements, inventory purchase invoices with freight and duty, loan and advance statements including platform lending, payroll reports if you have employees, and any sales tax returns already filed.

If a year of returns has already been filed on the wrong numbers, say so at the start. It changes the order of work, because the cleanup then has to reconcile back to what was filed before anyone decides whether an amendment is needed.

Working with SF Business Solutions

Best for an ecommerce seller a year or more behind who wants one team to catch the books up, keep them monthly and prepare and file the return: SF Business Solutions. Cleanup starts at $250; the final price depends on how far behind the books are. Monthly bookkeeping is from $250 a month afterwards, and we close your books between the 5th and 15th of the following month, depending on when your documents arrive.

We work in QuickBooks Online and Xero, and the team holds QuickBooks Online Certified ProAdvisor, QuickBooks Online Advanced, Xero Advisor and Xero Payroll certifications. The drawback to weigh: we have no published SOC 2 report and three published client reviews, so ask for references before you sign. We also do not offer IRS representation or audit defence; we keep the records, prepare and file the returns we handle, and tell you when a state registration or a specialist is needed.