Quick Overview
- 1#1: QuickBooks Online - Cloud-based accounting software with automated syncing of sales, inventory, and expenses from major ecommerce platforms like Shopify and Amazon.
- 2#2: Xero - Online accounting platform offering seamless integrations and bank reconciliations for multi-channel ecommerce businesses.
- 3#3: Zoho Books - Affordable cloud accounting solution with ecommerce features like automated sales imports and multi-currency support.
- 4#4: A2X - Automates accurate reconciliation of Amazon and Shopify payouts directly into QuickBooks or Xero for precise ecommerce bookkeeping.
- 5#5: Synder - Syncs sales, fees, and taxes from ecommerce platforms like Etsy, Shopify, and Amazon to your accounting software in real-time.
- 6#6: Webgility - Centralizes orders, inventory, and financials across ecommerce channels with automated accounting journal entries.
- 7#7: FreshBooks - User-friendly invoicing and bookkeeping tool with ecommerce integrations for small online stores.
- 8#8: Wave - Free accounting software with unlimited invoicing and payment processing ideal for bootstrapped ecommerce startups.
- 9#9: Sage Intacct - Scalable financial management platform with advanced ecommerce reporting and multi-entity support for growing businesses.
- 10#10: Brightpearl - Omnichannel commerce platform with integrated accounting for order-to-cash automation in ecommerce.
We evaluated tools based on features vital to e-commerce workflows (including platform syncing, inventory tracking, and multi-currency support), quality (reliability, accuracy, and user experience), ease of use (intuitive interfaces and minimal setup), and value (scalability, pricing flexibility, and long-term cost-effectiveness).
Comparison Table
Ecommerce bookkeeping requires tailored solutions to navigate sales channels, tax calculations, and transaction tracking effectively. This comparison table compares top tools like QuickBooks Online, Xero, Zoho Books, A2X, Synder, and more, examining features, pricing, and usability. Readers will discover which software best fits their business scale and specific needs.
| # | Tool | Category | Overall | Features | Ease of Use | Value |
|---|---|---|---|---|---|---|
| 1 | QuickBooks Online Cloud-based accounting software with automated syncing of sales, inventory, and expenses from major ecommerce platforms like Shopify and Amazon. | enterprise | 9.7/10 | 9.8/10 | 9.2/10 | 9.0/10 |
| 2 | Xero Online accounting platform offering seamless integrations and bank reconciliations for multi-channel ecommerce businesses. | enterprise | 9.2/10 | 9.5/10 | 9.0/10 | 8.7/10 |
| 3 | Zoho Books Affordable cloud accounting solution with ecommerce features like automated sales imports and multi-currency support. | specialized | 8.7/10 | 8.9/10 | 8.5/10 | 9.2/10 |
| 4 | A2X Automates accurate reconciliation of Amazon and Shopify payouts directly into QuickBooks or Xero for precise ecommerce bookkeeping. | specialized | 8.6/10 | 9.2/10 | 8.4/10 | 8.1/10 |
| 5 | Synder Syncs sales, fees, and taxes from ecommerce platforms like Etsy, Shopify, and Amazon to your accounting software in real-time. | specialized | 8.4/10 | 8.8/10 | 8.5/10 | 8.0/10 |
| 6 | Webgility Centralizes orders, inventory, and financials across ecommerce channels with automated accounting journal entries. | specialized | 8.3/10 | 9.1/10 | 7.6/10 | 8.0/10 |
| 7 | FreshBooks User-friendly invoicing and bookkeeping tool with ecommerce integrations for small online stores. | other | 7.4/10 | 6.8/10 | 9.2/10 | 7.5/10 |
| 8 | Wave Free accounting software with unlimited invoicing and payment processing ideal for bootstrapped ecommerce startups. | other | 7.6/10 | 6.8/10 | 9.4/10 | 9.7/10 |
| 9 | Sage Intacct Scalable financial management platform with advanced ecommerce reporting and multi-entity support for growing businesses. | enterprise | 8.2/10 | 8.8/10 | 7.4/10 | 7.1/10 |
| 10 | Brightpearl Omnichannel commerce platform with integrated accounting for order-to-cash automation in ecommerce. | enterprise | 7.8/10 | 8.7/10 | 7.1/10 | 7.0/10 |
Cloud-based accounting software with automated syncing of sales, inventory, and expenses from major ecommerce platforms like Shopify and Amazon.
Online accounting platform offering seamless integrations and bank reconciliations for multi-channel ecommerce businesses.
Affordable cloud accounting solution with ecommerce features like automated sales imports and multi-currency support.
Automates accurate reconciliation of Amazon and Shopify payouts directly into QuickBooks or Xero for precise ecommerce bookkeeping.
Syncs sales, fees, and taxes from ecommerce platforms like Etsy, Shopify, and Amazon to your accounting software in real-time.
Centralizes orders, inventory, and financials across ecommerce channels with automated accounting journal entries.
User-friendly invoicing and bookkeeping tool with ecommerce integrations for small online stores.
Free accounting software with unlimited invoicing and payment processing ideal for bootstrapped ecommerce startups.
Scalable financial management platform with advanced ecommerce reporting and multi-entity support for growing businesses.
Omnichannel commerce platform with integrated accounting for order-to-cash automation in ecommerce.
QuickBooks Online
enterpriseCloud-based accounting software with automated syncing of sales, inventory, and expenses from major ecommerce platforms like Shopify and Amazon.
Automatic syncing and reconciliation of sales data from ecommerce platforms like Shopify and Amazon
QuickBooks Online is a cloud-based accounting platform renowned for ecommerce bookkeeping, offering seamless integrations with platforms like Shopify, Amazon, WooCommerce, and BigCommerce to automatically sync sales, inventory, and payment data. It handles multi-channel sales tracking, automated transaction categorization, expense management, and sales tax calculations with tools like Avalara integration. Comprehensive reporting, invoicing, and real-time dashboards empower ecommerce businesses to maintain accurate books and make informed decisions without manual data entry.
Pros
- Seamless integrations with major ecommerce platforms for automated data import
- Robust inventory tracking and sales tax automation tailored for online sellers
- Advanced reporting and multi-currency support for global ecommerce operations
Cons
- Advanced features require higher-tier plans, increasing costs
- Steeper learning curve for complex inventory or multi-entity setups
- Customer support can be inconsistent during peak times
Best For
Ecommerce businesses from small online stores to scaling enterprises needing integrated bookkeeping across multiple sales channels.
Pricing
Starts at $30/month (Simple Start) up to $200/month (Advanced); annual billing offers 50% off first 3 months.
Xero
enterpriseOnline accounting platform offering seamless integrations and bank reconciliations for multi-channel ecommerce businesses.
Deep integrations with ecommerce platforms like Shopify and Amazon for automatic sales, inventory, and payment syncing
Xero is a cloud-based accounting software renowned for its robust integrations with major ecommerce platforms like Shopify, Amazon, WooCommerce, and Etsy, enabling seamless import of sales data, inventory levels, and payments for efficient bookkeeping. It offers automated bank reconciliation, multi-currency transactions, and detailed reporting for sales tax, GST/VAT compliance, and profitability analysis tailored to online sellers. With real-time dashboards and unlimited users, it simplifies financial management for growing ecommerce businesses without the need for manual data entry.
Pros
- Seamless integrations with top ecommerce platforms for automated data syncing
- Real-time bank feeds and reconciliation for accurate cash flow tracking
- Multi-currency support and customizable reporting for global sellers
Cons
- Basic inventory tracking requires third-party apps for advanced needs
- Higher-tier plans can become costly for high-volume transactions
- Payroll features limited or require add-ons in certain regions
Best For
Small to medium-sized ecommerce businesses needing strong platform integrations and automated bookkeeping for multi-channel sales.
Pricing
Starts at $15/month (Early plan) up to $78/month (Established plan) billed annually, with pay-as-you-go options and additional costs for apps.
Zoho Books
specializedAffordable cloud accounting solution with ecommerce features like automated sales imports and multi-currency support.
Automated sales data import and reconciliation from multiple ecommerce platforms like Shopify, Amazon, and Etsy
Zoho Books is a cloud-based accounting platform tailored for small to medium-sized businesses, with strong ecommerce bookkeeping capabilities including automated sales imports from platforms like Shopify, Amazon, and WooCommerce. It offers inventory tracking, multi-currency support, purchase orders, and bank reconciliation to streamline financial management for online sellers. Comprehensive reporting and automation features help ecommerce owners maintain accurate books without manual data entry.
Pros
- Seamless integrations with major ecommerce platforms for automatic sales and inventory syncing
- Robust inventory management and multi-channel order tracking
- Affordable pricing with scalable plans and a free tier for startups
Cons
- Advanced reporting and analytics are somewhat limited compared to enterprise tools
- Steeper learning curve for complex multi-location inventory setups
- Customer support response times can vary, especially on lower plans
Best For
Small to medium ecommerce businesses seeking an affordable, integrated solution for multi-channel sales bookkeeping.
Pricing
Free plan (up to $50K annual revenue); paid plans start at $20/month (Standard) up to $275/month (Ultimate), billed annually.
A2X
specializedAutomates accurate reconciliation of Amazon and Shopify payouts directly into QuickBooks or Xero for precise ecommerce bookkeeping.
Automated payout summaries that group thousands of transactions into a single, bank-matching journal entry for effortless reconciliation
A2X is an automated bookkeeping solution designed specifically for ecommerce businesses, reconciling sales data from platforms like Amazon, Shopify, eBay, and Stripe into accurate, summarized journal entries for accounting software such as Xero, QuickBooks, and MYOB. It handles complex payouts including fees, taxes, refunds, and discounts, eliminating manual reconciliation and reducing errors. By providing bank-matching reports, A2X ensures financial accuracy and saves significant time for growing online sellers.
Pros
- Precise automated reconciliation of ecommerce payouts matching bank deposits exactly
- Broad integration with major sales channels (Amazon, Shopify, etc.) and accounting tools
- Detailed reporting on fees, taxes, refunds, and net sales for compliant bookkeeping
Cons
- Pricing scales steeply with order volume, becoming costly for high-volume sellers
- Setup requires initial configuration and may involve a learning curve for non-accountants
- Lacks native accounting features, relying entirely on integrations
Best For
Mid-sized ecommerce sellers on multi-channel platforms who need automated, accurate payout reconciliation without manual data entry.
Pricing
Starts at $29/month (up to 100 orders) for Starter plan, scaling to $199+/month for higher volumes; annual discounts available, with enterprise custom pricing.
Synder
specializedSyncs sales, fees, and taxes from ecommerce platforms like Etsy, Shopify, and Amazon to your accounting software in real-time.
Payout reconciliation that automatically matches bank deposits from processors like Stripe and PayPal to detailed sales data
Synder is an automated bookkeeping tool tailored for e-commerce businesses, integrating with platforms like Shopify, Amazon, Etsy, and payment processors such as PayPal and Stripe. It syncs sales data, fees, refunds, taxes, and payouts directly into accounting software like QuickBooks Online, Xero, and Sage. This eliminates manual data entry, ensuring accurate reconciliation and real-time financial visibility for multi-channel sellers.
Pros
- Broad integrations with 20+ e-commerce platforms and accounting tools
- Smart rules for automatic categorization and multi-currency handling
- Real-time syncing reduces manual reconciliation time significantly
Cons
- Pricing scales per connection/store, which can get expensive for high-volume sellers
- Limited built-in reporting compared to dedicated analytics tools
- Occasional sync delays or errors reported with high transaction volumes
Best For
Multi-channel e-commerce merchants seeking automated data import and reconciliation into popular accounting software without complex setups.
Pricing
Free for 1 integration; Starter at $19/store/month (up to 1,000 orders), Pro at $49/store/month (unlimited orders) with advanced automation.
Webgility
specializedCentralizes orders, inventory, and financials across ecommerce channels with automated accounting journal entries.
Automated multi-channel sales reconciliation that deposits net sales, fees, and refunds directly into accounting ledgers
Webgility is an e-commerce integration platform designed to automate bookkeeping by syncing sales data from multiple channels like Shopify, Amazon, and Walmart directly into accounting software such as QuickBooks and Xero. It handles order management, inventory synchronization, and payment reconciliation to eliminate manual data entry and ensure accurate financial records. Ideal for scaling e-commerce businesses, it provides real-time reporting and reduces errors in multi-channel operations.
Pros
- Extensive integrations with 100+ e-commerce and accounting platforms
- Automated reconciliation of sales, fees, and taxes for accurate bookkeeping
- Real-time inventory and order syncing across channels
Cons
- Steep learning curve for initial setup and complex configurations
- Higher pricing tiers can be expensive for small single-channel sellers
- Limited built-in reporting compared to dedicated accounting tools
Best For
Multi-channel e-commerce businesses with moderate to high sales volume seeking automated sync to QuickBooks or Xero.
Pricing
Starts at $49/month for Starter (1 integration), $159/month for Professional (unlimited), and custom Enterprise pricing.
FreshBooks
otherUser-friendly invoicing and bookkeeping tool with ecommerce integrations for small online stores.
Seamless Shopify integration for automatic import of online sales and invoices
FreshBooks is a user-friendly cloud-based accounting software primarily designed for small businesses, freelancers, and service providers, focusing on invoicing, expense tracking, time management, and basic bookkeeping. For ecommerce bookkeeping, it offers integrations with platforms like Shopify, WooCommerce, Stripe, and PayPal to import sales data and automate bank reconciliations. While it handles basic transaction tracking and reporting effectively, it falls short on advanced inventory management, COGS calculations, and multi-channel sales consolidation compared to ecommerce-specialized tools.
Pros
- Intuitive interface ideal for non-accountants
- Strong integrations with Shopify and payment gateways like Stripe/PayPal
- Excellent mobile app for on-the-go expense tracking
Cons
- No native inventory tracking or COGS management
- Limited advanced ecommerce reporting and analytics
- Pricing scales quickly with client volume or advanced needs
Best For
Small ecommerce sellers or solopreneurs with simple sales channels who prioritize ease of use over complex inventory features.
Pricing
Lite ($19/mo, 5 clients), Plus ($33/mo, 50 clients), Premium ($60/mo, unlimited clients); annual billing offers 50% off first 3 months.
Wave
otherFree accounting software with unlimited invoicing and payment processing ideal for bootstrapped ecommerce startups.
100% free unlimited invoicing and core accounting with no user or transaction limits
Wave is a free cloud-based accounting platform tailored for small businesses and freelancers, providing invoicing, expense tracking, receipt scanning, and basic financial reporting. It connects to bank accounts and payment processors like Stripe and PayPal for transaction imports, making it viable for simple ecommerce bookkeeping. However, it lacks native inventory management and direct integrations with major ecommerce platforms like Shopify or Amazon, limiting it to basic reconciliation tasks.
Pros
- Completely free core accounting and unlimited invoicing
- Intuitive interface with mobile app support
- Automatic bank feeds and receipt scanning
Cons
- No inventory tracking or management
- Limited direct integrations with ecommerce platforms like Shopify
- Fees for payments (2.9% + $0.60) and payroll add-ons
Best For
Bootstrapped solopreneurs or small ecommerce sellers with simple sales volumes who need free basic bookkeeping without inventory needs.
Pricing
Free for accounting, invoicing, and reports; payments at 2.9% + $0.60 per credit card transaction; payroll starts at $20/month + $6/employee.
Sage Intacct
enterpriseScalable financial management platform with advanced ecommerce reporting and multi-entity support for growing businesses.
Multi-dimensional tracking and consolidation for precise revenue recognition across diverse ecommerce channels and subsidiaries
Sage Intacct is a robust cloud-based ERP and accounting platform designed for mid-market businesses, offering comprehensive financial management with strong ecommerce integrations via its marketplace. It automates bookkeeping processes like revenue recognition, inventory tracking, and multi-channel sales reconciliation, connecting seamlessly with platforms such as Shopify, Amazon, and BigCommerce. Ideal for scaling ecommerce operations, it provides dimensional reporting to track performance across sales channels, entities, and dimensions.
Pros
- Advanced multi-dimensional reporting for detailed ecommerce analytics
- Seamless integrations with major ecommerce platforms like Shopify and Amazon
- Scalable multi-entity management for growing online businesses
Cons
- Steep learning curve and complex setup requiring partners
- High pricing with custom quotes often exceeding $15K/year
- Less intuitive for small ecommerce teams without accounting expertise
Best For
Mid-sized ecommerce businesses with multiple sales channels or entities needing enterprise-grade financial controls and automation.
Pricing
Custom quote-based pricing, typically starting at $15,000 annually plus per-user/module fees; no public tiers.
Brightpearl
enterpriseOmnichannel commerce platform with integrated accounting for order-to-cash automation in ecommerce.
Real-time order-to-cash automation that unifies multi-channel ecommerce data with bookkeeping ledgers
Brightpearl is a cloud-based retail operating system designed for ecommerce businesses, providing integrated bookkeeping with inventory management, order fulfillment, and financial reporting. It automates reconciliation of multi-channel sales data with accounting ledgers, handling invoicing, payments, multi-currency transactions, and compliance like VAT/GST. This makes it suitable for scaling retailers needing unified operations and accurate financial visibility without separate accounting software.
Pros
- Seamless integration of ecommerce sales, inventory, and bookkeeping for real-time accuracy
- Strong multi-channel support and automated financial reconciliations
- Advanced reporting and compliance tools for growing retailers
Cons
- Steep learning curve due to comprehensive ERP-like interface
- High pricing not ideal for small businesses or startups
- Custom setup often requires professional services
Best For
Mid-sized ecommerce retailers with multiple sales channels needing integrated operations and bookkeeping.
Pricing
Custom quote-based pricing, typically starting at $500–$1,000+ per month depending on users, orders, and modules.
Conclusion
Selecting the right ecommerce bookkeeping software hinges on unique business requirements, but QuickBooks Online emerges as the top performer, delivering seamless synchronization with major platforms and automated tracking of sales, inventory, and expenses. Xero follows with strong multi-channel integration, while Zoho Books stands out for its affordability and multi-currency support—both are excellent alternatives for varying needs. These tools collectively simplify the complex task of managing ecommerce finances, ensuring accuracy and efficiency.
Explore QuickBooks Online today to experience its unmatched features, automate bookkeeping workflows, and set your ecommerce business up for financial success.
Tools Reviewed
All tools were independently evaluated for this comparison