Best Ecommerce Bookkeeping Software 2025
Ecommerce bookkeeping software automates multi-channel sales sync, COGS tracking, and marketplace fee reconciliation—saving sellers 2-20 hours monthly on accounting. Top solutions include A2X (Xero App of the Year, $29+/marketplace), Link My Books ($14+ for unlimited channels), and Finaloop (~$295/month for full-service).
This guide compares ecommerce accounting software by marketplace integrations, QuickBooks/Xero support, COGS tracking, and pricing. Find the right tool whether you sell on Amazon, Shopify, or across multiple channels.
Why Standard Accounting Fails Ecommerce
Ecommerce businesses face unique accounting challenges that QuickBooks and Xero alone cannot solve.
Manual Ecommerce Accounting Problems
- Thousands of individual transactions to enter manually
- Marketplace fees buried in settlement reports
- No separation of sales vs. refunds vs. fees
- Cannot track COGS at SKU level
- Multi-currency sales create confusion
- Settlement amounts don't match bank deposits
Ecommerce Software Solutions
- Summarized entries from settlement reports
- Automatic fee categorization (referral, FBA, etc.)
- Clean separation of revenue, refunds, fees
- SKU-level COGS and profitability tracking
- Multi-currency with auto exchange rates
- Deposits matched to accounting entries
Hours saved monthly
Businesses use A2X
Marketplace integrations
Essential Features for Ecommerce Sellers
Look for these capabilities when evaluating ecommerce bookkeeping software.
Multi-Channel Sync
Connect Amazon, Shopify, eBay, Etsy, Walmart
- Unified sales data
- Fee categorization
- Refund tracking
- Settlement matching
Inventory Management
Track stock across all channels
- Real-time updates
- Multi-location
- Low stock alerts
- Inventory valuation
COGS Tracking
SKU-level cost of goods sold
- Product costs
- Shipping fees
- FBA fees
- True margins
Fee Reconciliation
Separate marketplace fees from revenue
- Referral fees
- FBA fees
- Payment processing
- Returns costs
Financial Reports
P&L by channel and product
- Channel profitability
- SKU margins
- Cash flow
- Tax reports
Auto-Sync to Accounting
Push to QuickBooks, Xero, Sage
- Summary sync
- Per-transaction
- Bank matching
- Reconciliation
Ecommerce Bookkeeping Software Comparison
Compare leading solutions by integrations, accounting support, and pricing.
| Software | Best For | Pricing | Accounting | COGS |
|---|---|---|---|---|
| A2X | Multi-channel sellers, accountants | $29+/month per marketplace | QuickBooks, Xero, Sage, NetSuite | Basic |
| Link My Books | Multi-marketplace sellers | $14+/month (unlimited channels) | QuickBooks, Xero | Basic |
| Finaloop | DTC brands needing full-service | ~$295/month | Proprietary (replaces QuickBooks) | Advanced (SKU-level) |
| Synder | Multi-platform reconciliation | $42+/month | QuickBooks, Xero, Sage Intacct | Yes |
| Webgility | High-volume multi-channel | Custom pricing | QuickBooks, NetSuite | Advanced |
| QuickBooks Commerce | QuickBooks-first sellers | Bundled with QuickBooks | QuickBooks (native) | Basic |
A2X
$29+/month per marketplaceMulti-channel sellers, accountants
Amazon, Shopify, Walmart, eBay, Etsy, BigCommerce
Pros
- Xero App of the Year
- Summary sync
- Accurate fee breakdown
- Accountant trusted
Cons
- Per-marketplace pricing
- No inventory
- Setup complexity
Link My Books
$14+/month (unlimited channels)Multi-marketplace sellers
Amazon, eBay, Etsy, Shopify, Walmart, WooCommerce, TikTok Shop
Pros
- Unlimited marketplaces
- Free 1:1 onboarding
- Automatic VAT/GST
- Affordable
Cons
- No Sage/NetSuite
- Fewer advanced features
- Smaller user base
Finaloop
~$295/monthDTC brands needing full-service
Shopify, Amazon, WooCommerce, BigCommerce
Pros
- Full-service bookkeeping
- Real-time financials
- Expert support
- SKU profitability
Cons
- Higher cost
- Replaces traditional accounting
- Fewer marketplace integrations
Synder
$42+/monthMulti-platform reconciliation
30+ payment platforms, Shopify, Amazon, Stripe
Pros
- Payment platform focus
- Per-transaction or summary
- COGS sync
- Tax mapping
Cons
- Less marketplace-specific
- Complex setup
- UI learning curve
“My clients send me all kinds of messy PDFs from different banks. This tool handles them all and saves me probably 10 hours a week.”
Ashish Josan
Manager, CPA at Manning Elliott
Complete Your Ecommerce Stack with Zera Books
While ecommerce software syncs marketplace data, Zera Books processes bank statements, invoices, and financial documents for reconciliation.
Bank Statement Processing
Convert bank statements from any bank to Excel, CSV, or QBO to reconcile with marketplace settlements.
Supplier Invoice Extraction
Extract data from supplier invoices for accurate COGS calculation and inventory valuation.
Multi-Account Reconciliation
Process statements from multiple bank accounts used for different sales channels.
$79/month unlimited processing
Ecommerce Bookkeeping FAQs
Streamline Your Ecommerce Accounting
Zera Books converts bank statements and financial documents into clean data for reconciliation with your ecommerce accounting software.
Try for one week