For an online seller, the accounting software is only half the answer. The other half is the connector that gets Shopify, Amazon and other payouts into it correctly. I'm A2X certified and work in QuickBooks Online, so here's the setup I'd recommend at each stage, and where the alternatives fit.
Quick picks: most sellers → QuickBooks Online plus A2X. Want one entry per order instead of per payout → Webgility or Synder. Selling across borders with VAT → look hard at Link My Books. Just starting with a few sales a month → QuickBooks Online and a careful monthly summary entry.
Step one: the ledger
QuickBooks Online is where most US sellers should keep their books. Every CPA knows it, and it has the widest set of ecommerce connectors. Its Plus and Advanced plans add inventory tracking and classes, which help once you sell physical products across more than one channel. QuickBooks
Xero is the main alternative, with unlimited users and strong multi-currency support, and the same connectors work with it. Fewer US CPAs use it day to day, so ask yours first. My QuickBooks Online vs Xero comparison covers the trade-offs.
Step two: the connector (this is what most sellers are missing)
Shopify, Amazon and the other marketplaces pay you in batches, net of fees, refunds and adjustments. Book the deposit as sales and your revenue is understated and your fees vanish. A connector fixes that. The main difference between them is whether they post one summary per payout or every order.
| Connector | How it posts | Best for | Watch out for |
|---|---|---|---|
| A2X | One summarized entry per payout, matched to the deposit | Shopify and Amazon sellers who want clean, reconcilable books | Plans are priced by order volume |
| Link My Books | Summary per payout | Sellers with VAT and cross-border tax complexity | Built with UK and VAT sellers in mind |
| Synder | Summary or per-transaction, your choice | Multichannel sellers with many payment platforms | Per-transaction mode fills the ledger fast |
| Webgility | Order by order, in near real time | Sellers who need order-level detail, including B2B invoices | More setup; more transactions to review |
Why I default to A2X
For most sellers, summary posting is the right call. Each payout becomes one entry that splits out sales, refunds, shipping, fees and taxes, and because it totals exactly what hit the bank, it matches the deposit in one click. Your P&L shows gross sales and real margins, and your ledger stays readable. A2X supports Shopify, Amazon, eBay, Etsy, Walmart, PayPal and more, and posts to QuickBooks Online and Xero. I explain how it works in What is A2X? A2X
When order-level detail is worth it
If you invoice wholesale customers on terms, need per-order profitability inside the ledger, or your accountant insists on it, an order-level connector like Webgility makes sense. Just know that thousands of orders a month means thousands of transactions to keep clean. Webgility
Setup mistakes that break ecommerce books
- Everything in one sales account. Split gross sales, refunds, shipping income, platform fees and advertising.
- Marketplace-collected sales tax in revenue. Amazon and other marketplaces collect and remit sales tax in many states. Map it so it doesn't inflate your sales. See sales tax nexus explained.
- A start date that double-counts. Start the connector from the last reconciled date.
- No clearing accounts. Shopify Payments, PayPal and each marketplace need their own, so each payout ties out.
- Ignoring COGS. Without cost of goods sold, gross margin is fiction. Connectors like A2X can post COGS if you load product costs.
For the full workflow, read bookkeeping for ecommerce.
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