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Marketplace fees, refunds, and inventory make e-commerce books uniquely messy. We turn payout statements into clean, accurate books so you know your real profit per channel.
Bookkeeping shaped to how your business actually operates.
We decode Shopify, Amazon, and Stripe payouts so every fee and refund is recorded correctly.
Cost of goods tracked properly so your true margin is never a guess.
See which channel actually makes money, not just total sales.
Books structured to handle multi-state sales tax and nexus.
A simple, reliable process from first call to monthly reporting.
We connect to your accounting software and payment systems.
Transactions are categorized to fit your industry.
Every account is reconciled and verified monthly.
You get clear reports and a dedicated bookkeeper.
The services this industry most often needs, plus where to go next.
E-commerce accounting guide
Online sellers get paid through Shopify, Amazon, Etsy, Walmart, PayPal and Stripe. Each pays out on its own schedule, net of its own fees. E-commerce bookkeeping pulls all of that into one accurate set of books.
Every payout mixes gross sales, discounts, shipping income, refunds, fees and sometimes sales tax. Record each part separately, then match the net payout to the bank. Tools like A2X automate this for Shopify and Amazon.
| Channel | Typical costs to track |
|---|---|
| Own store (Shopify, WooCommerce) | Payment processing, apps, shipping, ads |
| Amazon | Referral fees, FBA fulfillment, storage, advertising |
| Etsy / Walmart / eBay | Listing or referral fees, payment processing, promoted listings |
Track revenue and fees by channel to see where your real margin is. See our Shopify and Amazon seller pages.
Include freight, duties and prep in each unit's cost, and expense it through cost of goods sold only when it sells. Check margins with the free profit margin calculator.
Marketplaces like Amazon, Etsy and Walmart collect and remit sales tax as marketplace facilitators. Sales through your own store may create obligations in each state where you pass economic nexus thresholds (often $100,000 in sales). See sales tax nexus explained.
Payment platforms issue Form 1099-K when payments exceed $20,000 and 200 transactions. Your books, not the 1099-K, are the basis for reporting income, so keep them reconciled. More in our e-commerce bookkeeping guide.
General information as of 2026, not tax advice. Confirm state rules with your tax preparer.
Related guides
Quick answers for your industry.
Marketplace payouts bundle sales, fees, refunds, and shipping into one deposit, and inventory must be tracked as cost of goods. Recording the net deposit alone hides your real numbers, so e-commerce books need careful reconstruction of each payout.
Yes. We reconcile Shopify, Amazon, Stripe, PayPal, and other processors, and connect them cleanly to QuickBooks or Xero.
We structure your books to track sales tax by state so you stay on top of economic nexus, and we work alongside your tax professional on filings.
Break each payout into gross sales, refunds, fees, shipping and sales tax, record those separately, and match the net amount to the bank deposit. Tools like A2X can automate the summaries.
Marketplaces collect it on their platforms in states that require it. For sales on your own store, you may need to register and collect in states where you pass economic nexus thresholds.
Under current law, payment platforms issue a 1099-K when your gross payments exceed $20,000 and 200 transactions in a year. All income is reportable regardless.
Book a free 15-minute consultation and see exactly how we would handle your bookkeeping.
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