Best accounting software for ecommerce and online sellers
Selling online looks simple from the outside: list a product, someone buys it, money lands in your bank. The books tell a different story. The deposit that shows up is never what your customers paid, your platform takes a stack of fees you can barely see, your stock moves in and out across more than one channel, and sales tax follows rules that change depending on where your buyer lives. Pick the wrong tool and you spend your evenings untangling all of it by hand.
This guide is about choosing accounting software that actually fits how ecommerce works, whether you sell on Shopify, Amazon, eBay, Etsy, or all of them at once. We'll cover the real problems: payouts that don't match your sales, the fee stack, inventory and cost of goods sold, sales tax across regions, and juggling more than one storefront. We'll be honest about what different tools do well, including where Argo Books fits and where it doesn't, so you can pick with your eyes open.
What online sellers actually need from accounting software
Before you compare tools, get clear on what an ecommerce business needs that a plain freelancer or service business doesn't. Miss any of these and you'll outgrow the software fast, or worse, file taxes on numbers that were wrong the whole time.
- A way to handle payouts that don't match your sales. Your platform pays you a lump sum every few days after fees, refunds, and shipping come out. Your software has to let you break that lump back into its parts.
- Fee tracking. Every sale carries selling fees and payment fees. They're small one at a time and large in a year, and every one is a deductible cost you don't want to miss.
- Inventory and cost of goods sold. If you buy or make physical products, you need to know what your stock cost and when that cost counts against your profit. This is the single biggest gap in tools built for service businesses.
- Sales tax tracking across regions. Selling online means selling into places you don't live, each with its own tax rules and thresholds.
- One home for multiple channels. Most sellers aren't on one platform. The totals from every storefront have to meet in one place.
Keep this list handy as you compare options. Some well-known tools nail invoicing and bank matching but have no real inventory. Others sync beautifully with one marketplace and charge a monthly fee that only makes sense at high volume. The right pick depends on your channels, your order count, and whether you sell physical goods. For a wider view of picking a tool, see our guide on the best accounting software for small business.
The payout problem: why your deposit never matches your sales
This is the thing that catches almost every new online seller. You made $2,000 in sales this week, but the deposit that hits your bank is $1,540. If you record that $1,540 as your income, your books are wrong in three ways at once: your sales look too low, your fees vanish, and any refunds hide inside the gap.
A single platform payout usually bundles all of this together: your gross sales, minus selling fees, minus payment processing fees, minus refunds you issued, minus shipping labels you bought, sometimes plus or minus a tax amount the platform collected. The bank only ever sees the final number. Good ecommerce bookkeeping means going back to the platform's settlement report, the detailed statement that shows every piece, and recording each part on its own.
So the question to ask any software is: can I take a settlement report and split it into gross sales, fees, refunds, and shipping? Some tools do this automatically by connecting to your marketplace. Many affordable tools, including Argo Books, don't auto-connect; instead you download the settlement or CSV report from your platform and import it, then split it out. Both approaches get you to correct books. The difference is how much of the splitting is done for you, which matters more the more orders you have. We go deep on this in our guide to bookkeeping for online sellers.
The fee stack, and why it decides your real margin
Every online channel takes a cut, and the cut is rarely just one fee. Recording only your payout as income hides all of it, and hidden fees mean both inaccurate books and lost deductions, because every one of these is a business cost you can write off.
- Selling or referral fees taken as a percentage of each sale. Amazon calls these referral fees, eBay calls them final value fees, Etsy calls them transaction fees. Same idea.
- Payment processing fees on top, usually a percentage plus a flat amount per order, whether that's Shopify Payments, Stripe, PayPal, or the marketplace's own processor.
- Listing or subscription fees such as Etsy's per-item listing charge, an eBay store subscription, or Amazon's monthly seller plan.
- Advertising fees from sponsored placements or offsite ads, which can be a chunky slice of a sale.
- Shipping label costs when you buy postage through the platform, netted straight out of your payout.
The right way to handle it is the same everywhere: record the gross sale as income, then record each fee type as its own expense, using the settlement report rather than the bank deposit as your source of truth. Do that and two things happen. You capture every deductible fee, which lowers your tax bill. And you finally see your real margin per sale, which is often a surprise. A product you thought cleared $12 might clear $7 once the selling fee, payment fee, and shipping are all counted. That's not bad news, it's the number you need to decide what's worth selling and what to raise the price on.
Inventory and cost of goods sold: the make-or-break feature
If you sell physical products, this is where a lot of accounting tools quietly fall short. Money you spend on stock isn't an expense the moment you buy it. It becomes a cost, cost of goods sold or COGS, only when the item actually sells. Software built for freelancers and service businesses often has no way to handle this at all, which means you either bolt on a spreadsheet or get your profit wrong.
Here's why it matters. Say you spend $4,000 restocking in November to get ready for the holidays, but only sell through half of it by year-end. If you deducted the whole $4,000 as a November expense, your books would show a loss that isn't real, because you still hold $2,000 of goods that are an asset, not a cost yet. That unsold stock stays as inventory until it sells. In most countries the tax rules require you to account for stock this way, and getting it right is what makes your profit honest instead of lumpy.
So look for software that tracks what stock you hold, what it cost, and what has sold, so it can calculate COGS for you. For a small seller a careful spreadsheet and a stock count at period-end works. As your product list and order volume grow, built-in inventory earns its keep fast. This is one area where Argo Books is genuinely strong: inventory and COGS are built in, not an add-on. Our guide on inventory tracking for small businesses goes deeper, and it applies just as much to a Shopify or eBay shop as to a physical store.
Sales tax across regions and channels
Sales tax is where ecommerce gets genuinely complicated, because selling online means selling into places you've never been. This is regional and it changes, so treat everything here as awareness, not advice, and confirm the specifics with your local tax authority or an accountant.
The core issue is that many tax systems require you to collect and remit sales tax, VAT, or GST once your sales into a region pass a threshold. In the United States that's the patchwork of state economic nexus rules; in the UK and EU it's VAT; in Canada it's GST and provincial taxes; and so on. The partial relief for online sellers is that large marketplaces increasingly collect and remit sales tax on your behalf in many regions, so Amazon or Etsy may handle the tax on sales made through them. But it isn't universal, and it usually won't cover sales through your own Shopify store or your own website, so you still need to know which sales were handled for you and which are yours to deal with.
The key bookkeeping habit is simple wherever you sell: record sales tax separately from your actual sales. The tax you collect is money you're holding to pass on, not income, and treating it as income is a classic way to accidentally spend money you owe. Software that tracks tax collected against tax paid and gives you a clean tax summary saves real headaches at filing time. Worth being clear about one thing: most affordable accounting tools, Argo Books included, track and summarise your sales tax but do not file or remit it for you. Some larger sellers use a dedicated sales-tax service that files across many states automatically. If that's you, factor it in as a separate cost.
Selling on more than one channel
Very few online sellers stay on a single platform. You might start on Etsy, add a Shopify store, list on eBay, and pick up Amazon along the way. Each channel has its own fee structure, its own settlement report, and its own quirks, and the whole point of accounting software is to bring them together so you see one business instead of four dashboards.
This is where two different kinds of tool split apart, and it's worth understanding the trade-off honestly:
- Connector and sync tools. Some services connect directly to Shopify, Amazon, and other marketplaces and pull sales, fees, and payouts in automatically, often splitting each settlement for you. If you push high order volume across several channels, the time this saves can easily justify a monthly fee, and it's the right call for a busy multi-channel seller. These usually cost more and still need checking, but they take the manual import out of your week.
- Import-based tools. Most affordable accounting apps, including Argo Books, don't auto-connect to marketplaces. Instead you download each platform's settlement or CSV report and import it, then split it into sales and fees. This takes more of your time per period, but it's cheaper, it keeps your data on your own machine, and for a seller doing tens or low hundreds of orders a month it's completely manageable.
Neither is wrong. The honest rule of thumb is volume. If you're a smaller or single-channel seller who doesn't mind a monthly import, an import-based tool keeps costs down. If you're running heavy volume across many channels and drowning in reports, a dedicated ecommerce-sync tool or connector is worth paying for. Be honest with yourself about which one you are before you buy.
Where Argo Books fits, and where it doesn't
Since this is our guide, here's a straight account of what Argo Books is good for as an ecommerce seller, and where a different tool would serve you better. The point is to help you choose well, not to talk you into the wrong fit.
Where Argo is a strong choice. It's free to start, so you can set up your books before you're making real money. It's a desktop app for Windows, Mac, and Linux that works offline, with your data living on your own machine, which many sellers prefer over cloud-only tools. Inventory and cost of goods sold are built in, so you can cost your products and track stock without a bolt-on. It has AI spreadsheet and CSV import, which is exactly how you bring in a platform's settlement report: export the CSV from Shopify, Amazon, eBay, or Etsy, import it, and let it help sort the rows. It tracks sales tax collected against tax paid and builds tax-ready reports. And it's cheap: Premium is $15 CAD a month or $150 a year, with a free tier that covers 25 invoices and 10 receipt scans a month. There's also a live Stripe integration, so if you take payments through Stripe you can pull sales, fees, and customers in directly.
Where Argo isn't the right fit. Be clear on this. Argo does not auto-sync with Etsy, Shopify, Amazon, or eBay. Stripe is the only live third-party integration; for every marketplace you import reports rather than connecting an account. It imports data, it isn't a continuous live bank feed. And it doesn't file or remit your taxes. So if you run very high order volume across several marketplaces and need each sale pulled in and split automatically, or you want hands-off multi-state tax filing, a dedicated ecommerce-sync tool or a specialist tax service will fit you better than Argo, and that's fine to say. But if you do your own books, sell at a manageable volume, want inventory and COGS built in, and would rather pay a little and own your data than pay a lot for automation you don't need yet, Argo is built for exactly that. If you sell handmade goods on Etsy specifically, our bookkeeping for Etsy sellers guide gets into the details that matter for makers.
Frequently asked questions
No, and it's important to be clear about that. Argo Books does not auto-connect to Shopify, Amazon, eBay, or Etsy. The only live third-party integration is Stripe, which pulls in your sales, fees, and customers directly. For the marketplaces, you export the settlement or CSV report from the platform and import it into Argo, using the AI spreadsheet import to help sort the rows into sales and fees. That takes a bit more of your time each period than an automatic sync, but it keeps the tool cheap and keeps your data on your own machine. If you run very high volume across many channels and need each sale pulled and split automatically, a dedicated ecommerce-sync connector will suit you better.
Because your platform takes fees, refunds, and shipping costs out of your sales before it pays you. A single payout usually bundles your gross sales, minus selling fees, minus payment processing fees, minus any refunds you issued, minus shipping labels you bought through the platform, and sometimes a tax amount too. Your bank only ever sees the final number. If you record that deposit as your income, your sales look too low and all your deductible fees disappear. The fix is to work from the platform's settlement report, not the bank deposit, and record the gross sale as income with each fee as its own expense. That gives you accurate books, captures every deduction, and shows your real margin per sale.
If you sell physical products, yes, or at least a solid stock spreadsheet. Money you spend on stock isn't an expense when you buy it; it becomes a cost only when the item sells. Without inventory tracking you can't calculate cost of goods sold correctly, which means your profit and your tax could both be wrong, especially if you buy stock in one period and sell it in another. Many tools built for freelancers or service businesses have no inventory feature at all, so this is worth checking before you commit. Argo Books has inventory and cost of goods sold built in. For a small seller a careful spreadsheet plus a period-end stock count also works until your volume grows.
It depends what you mean by handle. Most affordable tools, including Argo Books, track the sales tax you collect against the tax you pay and give you a tax summary, but they do not file or remit the tax for you. Filing is still your job or your accountant's. On top of that, large marketplaces like Amazon and Etsy increasingly collect and remit sales tax on your behalf in many regions, though usually not for sales through your own website or Shopify store, so you need to know which sales were handled for you. Rules and thresholds vary a lot by country and region, so confirm the specifics with your local tax authority or an accountant. High-volume sellers sometimes use a dedicated tax-filing service.
The goal is to get income and costs from every channel into one set of books, so your profit reflects the whole business rather than one storefront. There are two broad approaches. Connector tools link directly to your marketplaces and pull everything in automatically, which is worth the monthly cost if you run heavy volume across many channels. Import-based tools like Argo Books have you download each platform's settlement report and import it, then split it into sales and fees; this costs less and keeps your data local, and it's very manageable at tens or low hundreds of orders a month. Pick based on your order volume and how many channels you run. Be honest about which seller you are before paying for automation you may not need yet.