Best accounting software for online sellers (2026)
The right accounting software turns tax season from a panic into a 30-minute filing session. The wrong one — or none at all — means scrambling through bank statements in April trying to reconstruct a year of expenses you didn't track. Here's an honest comparison of the five tools online sellers actually use, with pricing, platform integrations, and a clear recommendation based on your selling situation.
In this guide
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Related guides: Etsy seller tax guide · Amazon FBA tax guide · Shopify seller tax guide · 1099-K explained · Reseller profit calculator
QuickBooks Online — #1 most CPA-compatible, connects to Etsy, Amazon, Shopify, and PayPal
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Wave — completely free invoicing, expense tracking, and financial reports
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FreshBooks — best invoicing + expense tracking, great for sellers who also do custom orders
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Xero — best for multi-channel sellers with complex inventory and multiple users
Try Xero Free →
What online sellers actually need from accounting software
Before comparing tools, here's what matters for e-commerce sellers specifically:
- Expense categorization that maps to Schedule C lines (COGS, advertising, shipping, platform fees)
- Platform integrations — automatic import from Etsy, Amazon, eBay, Shopify, PayPal, Stripe
- COGS and inventory tracking (critical for resellers and makers)
- 1099-K reconciliation — the ability to match your gross 1099-K against actual net income
- Quarterly tax estimates — so you know how much to set aside each quarter
- CPA access — your accountant can log in and see your books directly at tax time
QuickBooks Self-Employed — best for most sellers
QuickBooks Self-Employed
5/month
Best for: Active sellers on any platform who want automatic expense tracking and quarterly tax estimates.
What it does well: Automatic bank/card transaction import, expense categorization that maps directly to Schedule C, mileage tracking, quarterly tax estimate calculator, receipt capture via mobile app. The most CPA-compatible option — virtually every accountant works with QuickBooks.
Limitations: Not designed for inventory/COGS tracking (you'll need a separate system or upgrade to QuickBooks Online Simple Start at 5/month for inventory). Limited to one user. Price has increased over the years.
Platform integrations: Connects to Etsy, Amazon (via A2X add-on), Shopify, PayPal, Stripe, and all major banks.
What it does well: Automatic bank/card transaction import, expense categorization that maps directly to Schedule C, mileage tracking, quarterly tax estimate calculator, receipt capture via mobile app. The most CPA-compatible option — virtually every accountant works with QuickBooks.
Limitations: Not designed for inventory/COGS tracking (you'll need a separate system or upgrade to QuickBooks Online Simple Start at 5/month for inventory). Limited to one user. Price has increased over the years.
Platform integrations: Connects to Etsy, Amazon (via A2X add-on), Shopify, PayPal, Stripe, and all major banks.
Track expenses and estimate quarterly taxes automatically
QuickBooks Self-Employed categorizes your transactions as they happen and tells you exactly how much to set aside for taxes each quarter.
Try QuickBooks Self-Employed →Wave — best free option
Wave
Free (Starter) | 6/month (Pro)
Best for: New or small-volume sellers who want real accounting software without paying for it.
What it does well: The free Starter plan includes unlimited invoicing, expense tracking, bank connections, and basic financial reports. Wave Pro (6/month) adds receipt scanning, automatic transaction categorization, and automated late payment reminders. Unlimited users on all plans. Clean, simple interface that doesn't overwhelm non-accountants.
Limitations: No inventory or COGS tracking. No mileage tracking. Limited integrations compared to QuickBooks. Only available in the US and Canada. Customer support is limited on the free plan.
Platform integrations: Bank and credit card connections. Etsy/Amazon/eBay integration requires Zapier or manual CSV import.
What it does well: The free Starter plan includes unlimited invoicing, expense tracking, bank connections, and basic financial reports. Wave Pro (6/month) adds receipt scanning, automatic transaction categorization, and automated late payment reminders. Unlimited users on all plans. Clean, simple interface that doesn't overwhelm non-accountants.
Limitations: No inventory or COGS tracking. No mileage tracking. Limited integrations compared to QuickBooks. Only available in the US and Canada. Customer support is limited on the free plan.
Platform integrations: Bank and credit card connections. Etsy/Amazon/eBay integration requires Zapier or manual CSV import.
FreshBooks — best for service-heavy sellers
FreshBooks
1/month (Lite) | 8/month (Plus) | 5/month (Premium)
Best for: Sellers who also do custom orders, freelance design work, or consulting alongside their shop — anyone who invoices clients.
What it does well: Best invoicing features of any option (customizable templates, automatic reminders, client portal). Built-in time tracking for billable work. Strong mobile app. Expense tracking and receipt capture.
Limitations: The Lite plan only covers 5 clients. Not ideal for inventory-heavy businesses. More expensive than QuickBooks for similar features. Fewer CPA integrations.
Platform integrations: Stripe, PayPal, Shopify (via third-party). Less direct e-commerce integration than QuickBooks.
What it does well: Best invoicing features of any option (customizable templates, automatic reminders, client portal). Built-in time tracking for billable work. Strong mobile app. Expense tracking and receipt capture.
Limitations: The Lite plan only covers 5 clients. Not ideal for inventory-heavy businesses. More expensive than QuickBooks for similar features. Fewer CPA integrations.
Platform integrations: Stripe, PayPal, Shopify (via third-party). Less direct e-commerce integration than QuickBooks.
Get the accounting software comparison cheat sheet (PDF)
Side-by-side pricing table, feature matrix, and our recommendation based on selling platform and volume — on one printable page.
Xero — best for growing multi-channel businesses
Xero
0/month (Early) | 7/month (Growing) | 0/month (Established)
Best for: Multi-channel sellers who need unlimited users, inventory tracking, and strong international support.
What it does well: Unlimited users on every plan. Built-in inventory tracking. Strong multi-currency support. Over 1,000 app integrations including A2X (Amazon/Shopify bookkeeping automation), Cin7 (inventory), and Dear Systems. Modern interface.
Limitations: The cheapest plan (Early) limits you to 20 invoices and 5 bills per month — too restrictive for most sellers. The Growing plan at 7/month is the realistic starting point. Steeper learning curve than Wave or FreshBooks.
Platform integrations: A2X for Amazon and Shopify (best-in-class), Stripe, PayPal, Etsy (via Link My Books or Amaka).
What it does well: Unlimited users on every plan. Built-in inventory tracking. Strong multi-currency support. Over 1,000 app integrations including A2X (Amazon/Shopify bookkeeping automation), Cin7 (inventory), and Dear Systems. Modern interface.
Limitations: The cheapest plan (Early) limits you to 20 invoices and 5 bills per month — too restrictive for most sellers. The Growing plan at 7/month is the realistic starting point. Steeper learning curve than Wave or FreshBooks.
Platform integrations: A2X for Amazon and Shopify (best-in-class), Stripe, PayPal, Etsy (via Link My Books or Amaka).
Craftybase — best for handmade sellers (Etsy)
Craftybase
4.99/month (Starter) | 4.99/month (Pro)
Best for: Etsy makers, handmade sellers, and anyone who needs to track raw materials → finished products → COGS per item.
What it does well: Purpose-built for handmade sellers. Tracks raw materials, calculates COGS per product, imports Etsy/Shopify orders automatically, generates Schedule C–ready reports. Tracks Etsy fees broken down by type (listing, transaction, processing, Offsite Ads). The only tool that solves the handmade seller's biggest bookkeeping headache: material cost tracking across products.
Limitations: Not a full accounting platform — you may still need QuickBooks or Wave for your overall books. No invoicing, no payroll, no bank reconciliation. Niche tool, not a replacement for general accounting.
Platform integrations: Etsy (direct), Shopify (direct), WooCommerce, Amazon Handmade.
What it does well: Purpose-built for handmade sellers. Tracks raw materials, calculates COGS per product, imports Etsy/Shopify orders automatically, generates Schedule C–ready reports. Tracks Etsy fees broken down by type (listing, transaction, processing, Offsite Ads). The only tool that solves the handmade seller's biggest bookkeeping headache: material cost tracking across products.
Limitations: Not a full accounting platform — you may still need QuickBooks or Wave for your overall books. No invoicing, no payroll, no bank reconciliation. Niche tool, not a replacement for general accounting.
Platform integrations: Etsy (direct), Shopify (direct), WooCommerce, Amazon Handmade.
Track materials and COGS per product
Craftybase imports your Etsy sales, tracks material costs across products, and generates COGS reports ready for Schedule C.
Try Craftybase →Side-by-side comparison
| Feature | QuickBooks SE | Wave | FreshBooks | Xero | Craftybase |
|---|---|---|---|---|---|
| Starting price | 5/mo | Free | 1/mo | 0/mo | 5/mo |
| Expense tracking | ✓ | ✓ | ✓ | ✓ | ✗ |
| COGS / inventory | Limited | ✗ | Basic | ✓ | ✓ (best) |
| Quarterly tax est. | ✓ | ✗ | ✗ | ✗ | ✗ |
| Etsy integration | ✓ | Via Zapier | Via Zapier | Via A2X | ✓ (direct) |
| Amazon integration | Via A2X | Manual | Manual | Via A2X | Limited |
| CPA access | ✓ (best) | ✓ | ✓ | ✓ | ✗ |
| Best for | Most sellers | Budget | Invoicing | Multi-channel | Handmade/Etsy |
Our recommendation by seller type
- New seller, small volume, tight budget: Start with Wave (free). It handles the basics and you can upgrade later.
- Active seller on any platform: QuickBooks Self-Employed (5/month). Automatic expense tracking, quarterly estimates, and every CPA in America knows how to use it.
- Etsy maker tracking materials: Craftybase (5/month) for COGS + Wave (free) or QuickBooks for overall books. The combo solves both the material tracking and general accounting problems.
- Amazon FBA seller: Xero (7/month) + A2X (5–9/month). A2X automates the notoriously complex Amazon settlement report reconciliation. This combo is the gold standard for FBA bookkeeping.
- Shopify store owner: QuickBooks Online Simple Start (5/month) or Xero Growing (7/month) — both integrate with Shopify directly and handle inventory.
- Multi-platform seller: Xero Growing (7/month). Unlimited users, strong integrations across platforms, and the best multi-channel support.
The real cost of no accounting software
The average online seller who doesn't track expenses misses ,000–,000 in deductions per year. At a 25% effective tax rate, that's 50–,000 in unnecessary taxes — far more than the cost of any software on this list. The tool pays for itself many times over.
Beyond traditional accounting software, Amazon and Etsy sellers often benefit from dedicated profit-tracking tools. A2X automates the complex settlement-report reconciliation that trips up most Amazon sellers using QuickBooks or Xero — it splits payouts by COGS, fees, refunds, and ad spend before posting to your books.
From our network
Automate your Amazon bookkeeping
A2X splits every Amazon payout by fees, COGS, and refunds — so your Schedule C is accurate before you open tax software.
Read A2X Review →