Who this is for
Catch-Up Bookkeeping for E-commerce Sellers
The single biggest error in e-commerce books is treating a payout as a sale. A Shopify or Amazon payout is sales minus fees minus refunds minus sales tax collected, sometimes minus advertising, arriving days after the orders. Books built on payouts understate sales and hide fees entirely.
Payouts are not sales
The cleanup rebuilds income from the platform’s own reports: gross sales, discounts, refunds, fees, sales tax collected and the net paid out, for every settlement period. The bank then matches the net, and the profit and loss shows gross sales with fees as a cost rather than a smaller number nobody can explain. Where a 1099-K was issued, it reconciles to gross sales, which is the check a tax preparer will run.
Inventory and cost of goods sold
Product bought is not an expense until it sells. A seller who expenses every supplier invoice shows losses in buying months and windfalls in selling months, and a tax return built on that is wrong in both directions. The cleanup rebuilds cost of goods from purchases and whatever count exists, year by year, and sets up a method that can be kept from here on. If no count was ever taken, that is said plainly and the options are laid out for the preparer.
Sales tax and marketplace facilitators
Most marketplaces collect and remit sales tax on your behalf; a standalone store may not. The cleanup separates tax collected from sales, records what the platform remitted, and leaves what you owe as a liability. Which states require you to register is a question for your tax preparer or a sales tax specialist; the books carry whatever the answer is.
Multiple channels and one bank account
Amazon, Shopify, Etsy, eBay and a wholesale account all paying into one bank account is normal, and the cleanup gives each its own income and fee lines so channel margins can be compared. Advertising spent inside a platform is separated from advertising paid by card.
Send which platforms you sell on, how many months are behind, and whether a 1099-K was issued. The reply within a business day says what the deposit would be.
E-commerce Sellers: common questions
Can the books reconcile to my 1099-K?
Yes. Gross sales are rebuilt from platform reports, so the 1099-K figure ties to the books rather than to the bank deposits.
I never counted inventory. What happens?
Cost of goods is rebuilt from purchases and whatever evidence exists, and the gap is documented for your tax preparer rather than filled with a guess.
Do you connect to Shopify or Amazon directly?
Settlement reports are the source either way. Integrations can help going forward; for a catch-up the reports are more reliable.
What your bookkeeper handles
- QuickBooks Cleanup Services
- Catch-Up Bookkeeping Services
- Bookkeeping Cleanup Services
- Behind on Bookkeeping Before a Tax Deadline
- Multiple Years of Bookkeeping, Rebuilt
- Monthly Bookkeeping After the Cleanup
Also written for Sole Proprietors & Single-Member LLCs, S Corporations, Contractors & Trades, Restaurants & Food Businesses, Real Estate Agents & Brokers, Medical & Dental Practices and Switching From Another Bookkeeper.
Request a quote for your online store
Tell us how far behind the books are and whether there is a date. Your bookkeeper replies within one business day with a plain answer: what it would take, whether the date is reachable, and what the deposit would be. Requests answered within one business day · Calls Mon–Fri, 9am–5pm Eastern Or call (888) 786-6502 if you would rather talk it through first.