For an online seller, choosing ecommerce accounting software is only half the answer. The other half is the connector that gets Shopify, Amazon and other payouts into the books correctly. I'm A2X certified and work in QuickBooks Online, so here's the setup I'd recommend at each stage, a worked payout example, 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.
Ecommerce accounting software at a glance
| Tool | Best for | Handles well | Watch-outs |
|---|---|---|---|
| QuickBooks Online (ledger) | Most US sellers | What CPAs expect; the widest set of ecommerce connectors; inventory and classes on Plus and Advanced | Built-in inventory gets heavy with large catalogs |
| Xero (ledger) | Multi-currency sellers and larger teams | Unlimited users; strong multi-currency | Fewer US CPAs work in it day to day |
| A2X (connector) | Shopify and Amazon sellers who want clean, reconcilable books | One summary entry per payout, matched to the deposit; can post COGS | Plans are priced by order volume |
| Link My Books (connector) | Sellers with VAT and cross-border tax complexity | Summary per payout with VAT handling | Built with UK and VAT sellers in mind |
| Synder (connector) | Multichannel sellers with many payment platforms | Summary or per-transaction posting, your choice | Per-transaction mode fills the ledger fast |
| Webgility (connector) | Sellers who need order-level detail, including B2B invoices | Order-by-order posting in near real time | More setup; more transactions to review |
Step one: the ledger
Shopify's and Amazon's own reports aren't a ledger. They show what happened on that channel, not your whole business, so you still need real accounting software underneath.
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 wrong and your fees vanish. A connector fixes that. The main difference between them, shown in the table above, is whether they post one summary per payout or every order.
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
Worked example: booking a Shopify payout at gross
Here's what a connector does, with round numbers. This is a hypothetical store. Say one Shopify Payments payout lands in checking for $9,880. Behind that single deposit:
| Payout line | Amount |
|---|---|
| Gross product sales | $10,000 |
| Shipping charged to customers | $400 |
| Sales tax collected from customers | $600 |
| Refunds | −$800 |
| Shopify Payments processing fees | −$320 |
| Deposit to checking | $9,880 |
Book the $9,880 as sales and the total looks close enough to survive for months. But $600 of it is sales tax you owe the state, the $800 of refunds and $320 of fees disappear from the P&L, and you can't tell product revenue from shipping income.
A connector posts the same payout as one summary entry to a Shopify clearing account:
| Account | Debit | Credit |
|---|---|---|
| Shopify clearing | $9,880 | |
| Refunds and returns | $800 | |
| Merchant processing fees | $320 | |
| Sales | $10,000 | |
| Shipping income | $400 | |
| Sales tax payable | $600 | |
| Total | $11,000 | $11,000 |
When the $9,880 deposit shows up in the bank feed, you match it to the clearing account and the clearing balance goes back to zero. The P&L now shows $10,000 of gross sales, $800 of refunds (net sales of $9,200), $400 of shipping income and $320 of fees, and the $600 of tax sits on the balance sheet until it's paid. If your deposits never seem to tie to Shopify's sales report, here's why Shopify deposits don't match sales.
The same idea on Amazon
Amazon takes more out before it pays you. Say a two-week Amazon settlement deposits $6,250:
| Settlement line | Amount |
|---|---|
| Product sales | $10,000 |
| Refunds | −$500 |
| Referral fees | −$1,500 |
| FBA fulfillment fees | −$1,250 |
| Advertising charged against the balance | −$500 |
| Sales tax collected by Amazon, then withheld by Amazon | $700 − $700 = $0 |
| Deposit to checking | $6,250 |
Booked as sales, that deposit understates revenue by $3,750 and hides $3,250 of selling costs. Posted at gross, the P&L shows $10,000 of sales, $500 of refunds, and the referral fees, fulfillment fees and ads in their own expense accounts. That's the only way to see what Amazon costs you as a channel.
Selling on more than one channel
Every place that pays you needs its own clearing account: Shopify Payments, PayPal, Amazon, Etsy, Walmart, eBay, and wholesale customers through accounts receivable. Each connector entry lands in its channel's clearing account, and each deposit clears it. A clearing balance that won't go back to zero is a signal: a missing payout, a reserve the platform is holding, or a deposit that went to a different bank account.
To see profit by channel, keep one set of income and fee accounts and tag each entry by channel with classes or locations in QuickBooks Online Plus or Advanced, instead of building a separate chart of accounts for every channel. And treat gift cards as a liability when you sell them and as revenue when they're redeemed, not as sales on day one.
Inventory and cost of goods sold
Inventory you've paid for but haven't sold is an asset on the balance sheet, including stock sitting in Amazon's fulfillment centers. It becomes cost of goods sold when it sells. Without COGS, your gross margin is a guess. There are three workable ways to get it into the books:
- From the connector. Load product costs into A2X and it posts COGS with each payout based on units sold. Good for small and mid-size catalogs where costs don't change often.
- From QuickBooks inventory. QuickBooks Online Plus and Advanced track quantities by item using FIFO. It works with a modest number of SKUs; large catalogs with variants and several warehouses get heavy fast.
- From a periodic count. Count inventory at month or quarter end and post one adjusting entry, so COGS equals beginning inventory plus purchases minus ending inventory. Simple, but your margins are only right on count dates.
Ask your CPA which costs belong in inventory (freight and duties on purchases usually come up) and which inventory method the tax return uses. Those are their call. Keeping the counts and costs clean is ours.
Marketplace-collected sales tax (and the tax that's still yours)
Under marketplace facilitator laws, Amazon, Etsy, Walmart and eBay collect and remit sales tax on most sales made through them. In the settlement, that tax shows up twice: collected from the buyer, then withheld by the marketplace. Map both lines to the same account so they net to zero and never touch sales.
Your own Shopify store is different. There you're generally the seller, so the tax your customers pay is inside your payout and you owe it to every state where you have nexus. Book it to sales tax payable, and whoever files your sales tax returns pays it from there. We don't file sales tax returns. We make sure the liability on the balance sheet matches what was collected, so the filer starts from a clean number. If you're not sure where you have nexus, start with sales tax nexus explained.
How to choose the best accounting software for ecommerce
- Ask your CPA which ledger they want. For most US sellers that's QuickBooks Online. If they're happy in Xero and you need multi-currency or many users, Xero works with the same connectors.
- List every place money comes in. Shopify Payments, PayPal, each marketplace, wholesale. Make sure your connector covers all of them, or plan for two.
- Count your orders in your busiest month. Connector plans are usually priced by order volume, so check the vendor's current pricing against your peak, not an average month.
- Pick summary or order-level posting. Summary per payout for most sellers; order-level if you invoice wholesale customers on terms or need per-order detail in the ledger.
- Decide how COGS gets in. Connector, QuickBooks inventory or a periodic count, based on the size of your catalog.
- Set the start date carefully. Start the connector the day after your last reconciled date. If the books are behind, catch them up first, or the connector posts clean entries into a messy ledger.
Setup mistakes that break ecommerce books
- Everything in one sales account. Split gross sales, refunds, shipping income, platform fees and advertising.
- Deposits booked as sales. The total looks close, but tax, refunds and fees disappear, as the example above shows.
- Marketplace-collected sales tax in revenue. It was never yours. Map it so it nets to zero.
- A start date that double-counts. Start the connector from the last reconciled date.
- Ignoring COGS. Without cost of goods sold, gross margin is fiction.
For the full workflow, read bookkeeping for ecommerce.
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