Choose the Right Accounting Software
Proper accounting software is essential for online sellers. Manual spreadsheets work for side hustles, but once you're doing $50K+ annually or selling across multiple platforms, you need automation. These tutorials walk you through setup, integration, and best practices for the top e-commerce accounting platforms.
All platforms covered here: Integrate with Amazon, Shopify, Etsy, eBay, and Walmart. Automate sales tracking, fee reconciliation, inventory management, and tax reporting.
QuickBooks Online
Industry-leading accounting for growing e-commerce businesses
Best For
- Sellers doing $100K+ annually
- Multi-platform sellers (Amazon, Shopify, etc.)
- Businesses with inventory management needs
- Those who need CPA compatibility
Key Features
- Real-time sales & expense tracking
- Automatic bank reconciliation
- Inventory tracking & COGS automation
- 1099-K reconciliation
- Multi-user access (team collaboration)
- Integrates with 400+ apps
$30-$200/month depending on plan (Simple Start, Essentials, Plus, Advanced)
Xero
Beautiful cloud accounting with powerful e-commerce integrations
Best For
- International sellers (multi-currency support)
- Amazon FBA sellers
- Businesses prioritizing ease of use
- Those wanting mobile-first accounting
Key Features
- Unlimited users on all plans
- Real-time dashboard & cash flow tracking
- Automatic Amazon FBA reconciliation
- Inventory management built-in
- Multi-currency & international support
- Beautiful reporting & analytics
$13-$80/month (Early, Growing, Established plans)
Wave Accounting
100% free accounting software for small sellers
Best For
- New sellers (under $50K annually)
- Side hustles & part-time sellers
- Budget-conscious entrepreneurs
- Single-channel sellers
Key Features
- 100% free core accounting features
- Invoicing & payment processing
- Receipt scanning & expense tracking
- Bank connections & reconciliation
- Basic financial reports
- Mobile app access
Free! (Optional paid add-ons for payroll & payments)
FreshBooks
Simple accounting with powerful invoicing for service-based sellers
Best For
- Service-based sellers (consulting, design)
- Freelancers selling digital products
- Businesses prioritizing invoicing
- Small teams (1-10 people)
Key Features
- Professional invoicing & estimates
- Time tracking & project management
- Expense tracking & categorization
- Client portal & payment processing
- Automated late payment reminders
- Tax-ready reports
$19-$60/month (Lite, Plus, Premium plans)
Side-by-Side Comparison
| Feature | QuickBooks | Xero | Wave | FreshBooks |
|---|---|---|---|---|
| Price (Monthly) | $30-$200 | $13-$80 | Free | $19-$60 |
| Best For | Growing businesses $100K+ | Amazon FBA & international | New sellers under $50K | Service-based sellers |
| Multi-User Access | Yes (3-25 users) | Unlimited | No | Yes (up to 500) |
| Inventory Tracking | Yes (Plus & above) | Yes | No | No |
| E-commerce Integrations | 400+ apps | 300+ apps | Limited | 100+ apps |
| Amazon FBA Support | Yes (via Link My Books) | Yes (native & apps) | No | Limited |
| Multi-Currency | Yes (Plus & above) | Yes (all plans) | Limited | Yes |
| Mobile App | Yes | Yes | Yes | Yes |
| CPA Preferred | Yes (industry standard) | Yes | Less common | Somewhat |
Essential E-commerce Integrations
These apps bridge the gap between your sales platforms and accounting software:
Link My Books
Automates Amazon & Shopify to QuickBooks/Xero. Handles fees, refunds, 1099-K reconciliation. $99-299/month.
A2X Accounting
Connects Amazon, Shopify, eBay to QuickBooks/Xero. Best-in-class for multi-channel sellers. $199-499/month.
Amazon Seller Central
Direct integrations available in QuickBooks & Xero. Free but requires manual setup and maintenance.
Shopify Native
QuickBooks & Xero both offer native Shopify sync. Real-time orders, payouts, and inventory updates.
TaxJar
Automates sales tax calculation and filing. Integrates with all major accounting platforms. $19-499/month.
ShipStation
Connects shipping & fulfillment data to accounting software. Tracks shipping costs as expenses automatically.
Pro Tips for Using Accounting Software
Start Simple
Don't over-customize at first. Use default settings and templates. Learn the basics before advanced features.
Reconcile Weekly
Bank reconciliation should be weekly, not monthly. Catch errors early before they compound.
Use Categories Consistently
Set up a chart of accounts once and stick to it. Consistency makes year-over-year comparisons accurate.
Automate Everything
Enable auto-import for bank feeds, sales platforms, and credit cards. Manual entry = errors.
Backup Regularly
Export your data monthly. Cloud software is reliable, but always maintain your own backups.
Work with a CPA
Once revenue exceeds $100K, hire a CPA. They'll optimize your setup and save you thousands in taxes.
Ready to Get Started?
Choose your software above and start automating your accounting today. Most offer free trials—test before committing.
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