Best Accounting Software for Ecommerce in 2026

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What ecommerce sellers need from accounting software

An online store makes more transactions than most service businesses: orders, refunds, payouts, fees and stock movements, often across several channels. When you compare tools, check these:

• Inventory and cost of goods sold — stock levels and what each sale actually cost you.
• Sales channel connections — Shopify, Amazon, Etsy, eBay, and how many channels your plan allows.
• Orders and purchasing — sales orders, purchase orders and shipping labels.
• Sales tax or VAT — US economic nexus tracking, or UK MTD VAT.
• Multi-currency — if you sell abroad or buy from overseas suppliers.
• Price at the tier you need — not the headline entry price.

Facts below come from official pricing pages; we haven’t run a hands-on test for this article. To see the right plan for your country and features, use the finder and pick “Ecommerce”.

Which plan unlocks what (US)

Monthly list prices in USD before promotions. Xero’s pricing page lists Inventory Plus as optional on Growing and Established but doesn’t show the add-on’s own price, so confirm it at checkout.

QuickBooks Online: best all-in-one for US sellers

QuickBooks puts everything a product seller needs into one tier: Plus. On its US plan comparison, Plus adds inventory tracking, purchase orders, sales orders, item receipts and shipping labels, and connects all sales channels. Simple Start connects 1 channel and Essentials 3. Automatic sales tax and economic nexus tracking start on Simple Start, which matters if you sell into many US states.

Xero + Inventory Plus: best for Shopify & Amazon sellers

Xero’s US answer for ecommerce is Xero Inventory Plus, an add-on for the Growing ($59) and Established ($97) plans. Xero says it connects to Shopify and Amazon (FBA) and keeps stock in sync across channels and your own website. It also handles online purchase orders with partial receipts, shipping rates, labels and returns, and gives you an inventory dashboard of profit by channel.

Two caveats. The pricing page lists Inventory Plus as optional but doesn’t show what it costs, so check before you commit. It’s also a US product; elsewhere you’ll rely on Xero’s app marketplace for ecommerce connections. The upside is Xero’s no-per-user-fee pricing, handy when a warehouse helper and a bookkeeper both need access.

See Xero’s current offer (partner link, opens in a new tab)

Zoho Books: best value as you grow

Zoho Books spreads ecommerce features across tiers, which keeps early costs low. On its US plan comparison, Professional ($50, or $40 billed yearly) adds stock tracking, sales and purchase orders, price lists and base-currency adjustments. Elite ($150, or $120 yearly) is where marketplaces arrive: it connects Etsy, eBay and Amazon plus up to 2 Shopify stores, prints shipping labels, and adds composite items and bin locations.

That makes Zoho a natural fit for a seller who starts with one store and manual stock counts, then grows into multi-channel. Just note the jump from Professional to Elite is large ($50 to $150 a month). As with every Zoho edition, the country you choose at sign-up can’t be changed later.

Try Zoho Books (partner link, opens in a new tab)

Sage Accounting: best for UK online retailers

For a UK shop, Sage Accounting Plus (£59 a month, excluding VAT) is described by Sage as the plan “for small businesses managing inventory or working in multiple currencies”. It comes with unlimited users and payroll included. Every Sage Accounting UK plan handles MTD-compatible VAT returns. Full details in our Sage Accounting review.

Sales channel connections aren’t listed on Sage’s pricing page, so check the integrations you need. UK sellers should also compare Zoho Books UK Professional (£24, or £20 yearly), which adds inventory and multi-currency; see our UK MTD guide.

Tools that aren’t built for product sellers

• FreshBooks — great for service businesses, but inventory isn’t on its pricing page and plans are capped by billable clients. See our freelancer guide instead.
• Wave — free invoicing and bookkeeping for US and Canadian businesses. Inventory and marketplace connections aren’t on its pricing page.
• QuickBooks Free / Zoho Books Free — fine for a side hustle, but stock tracking needs a paid tier (QuickBooks Plus, Zoho Professional). More in our free software guide.

Not selling online, or need inventory outside the US? See the cheapest accounting software with inventory by country.

Which one should you choose?

• US seller on several channels, wants one plan for everything: QuickBooks Online Plus.
• Shopify or Amazon seller with a small team: Xero Growing + Inventory Plus.
• Starting small, growing into marketplaces: Zoho Books Professional, then Elite.
• UK online shop with staff: Sage Accounting Plus, or Zoho Books UK Professional on a budget.
• Deciding between the two biggest names? Read Xero vs QuickBooks.

Janak Bahadur Uparkoti

Founder & Software Researcher

Janak researches SaaS tools, free trials, pricing plans, and small-business software workflows. He focuses on helping small business owners compare accounting tools clearly before purchasing.

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