Quick Overview
- 1#1: A2X - Automates reconciliation of Amazon and Shopify seller payouts directly to accounting software like Xero and QuickBooks.
- 2#2: Link My Books - Syncs and reconciles sales and payments from Shopify, Amazon, Etsy, and more to Xero or QuickBooks Online.
- 3#3: Synder - Automatically syncs ecommerce transactions from multiple platforms to QuickBooks or Xero for seamless bank reconciliation.
- 4#4: PayTraqer - Provides automated daily reconciliation of Shopify payments, fees, refunds, and taxes to accounting software.
- 5#5: Finaloop - Automates end-to-end bookkeeping and payment reconciliation for Amazon, Etsy, and Walmart sellers.
- 6#6: Webgility - Integrates ecommerce sales data across channels for automated accounting sync and payment reconciliation.
- 7#7: TrueProfit - Tracks ecommerce profitability by reconciling bank transactions, fees, and payouts from various platforms.
- 8#8: BeProfit - Calculates real-time P&L by automatically reconciling ecommerce sales, costs, and payment gateway data.
- 9#9: Pipe17 - Centralizes order and inventory data from ecommerce platforms for accurate financial reporting and reconciliation.
- 10#10: ReconArt - Cloud-based platform for automating payment, bank, and account reconciliation suitable for ecommerce operations.
Tools were chosen based on depth of integrations, precision in reconciling diverse transaction types (fees, refunds, taxes), user experience, and value in automating complex financial processes.
Comparison Table
Ecommerce businesses require effective payment reconciliation tools to manage transactions, track discrepancies, and simplify financial processes. This comparison table explores top solutions including A2X, Link My Books, Synder, PayTraqer, Finaloop and more, examining features, integration strengths, and user-friendly design. Readers will discover key differentiators to choose software that fits their operational needs and budget.
| # | Tool | Category | Overall | Features | Ease of Use | Value |
|---|---|---|---|---|---|---|
| 1 | A2X Automates reconciliation of Amazon and Shopify seller payouts directly to accounting software like Xero and QuickBooks. | specialized | 9.7/10 | 9.9/10 | 9.4/10 | 9.2/10 |
| 2 | Link My Books Syncs and reconciles sales and payments from Shopify, Amazon, Etsy, and more to Xero or QuickBooks Online. | specialized | 9.2/10 | 9.5/10 | 9.1/10 | 8.9/10 |
| 3 | Synder Automatically syncs ecommerce transactions from multiple platforms to QuickBooks or Xero for seamless bank reconciliation. | specialized | 8.7/10 | 9.2/10 | 8.5/10 | 8.0/10 |
| 4 | PayTraqer Provides automated daily reconciliation of Shopify payments, fees, refunds, and taxes to accounting software. | specialized | 8.7/10 | 9.2/10 | 8.5/10 | 8.3/10 |
| 5 | Finaloop Automates end-to-end bookkeeping and payment reconciliation for Amazon, Etsy, and Walmart sellers. | specialized | 8.5/10 | 9.2/10 | 8.3/10 | 7.9/10 |
| 6 | Webgility Integrates ecommerce sales data across channels for automated accounting sync and payment reconciliation. | enterprise | 8.2/10 | 8.7/10 | 7.8/10 | 7.9/10 |
| 7 | TrueProfit Tracks ecommerce profitability by reconciling bank transactions, fees, and payouts from various platforms. | specialized | 8.4/10 | 8.7/10 | 8.9/10 | 8.0/10 |
| 8 | BeProfit Calculates real-time P&L by automatically reconciling ecommerce sales, costs, and payment gateway data. | specialized | 8.4/10 | 8.6/10 | 8.2/10 | 8.3/10 |
| 9 | Pipe17 Centralizes order and inventory data from ecommerce platforms for accurate financial reporting and reconciliation. | enterprise | 6.9/10 | 6.2/10 | 8.1/10 | 6.4/10 |
| 10 | ReconArt Cloud-based platform for automating payment, bank, and account reconciliation suitable for ecommerce operations. | enterprise | 8.1/10 | 8.7/10 | 7.4/10 | 7.8/10 |
Automates reconciliation of Amazon and Shopify seller payouts directly to accounting software like Xero and QuickBooks.
Syncs and reconciles sales and payments from Shopify, Amazon, Etsy, and more to Xero or QuickBooks Online.
Automatically syncs ecommerce transactions from multiple platforms to QuickBooks or Xero for seamless bank reconciliation.
Provides automated daily reconciliation of Shopify payments, fees, refunds, and taxes to accounting software.
Automates end-to-end bookkeeping and payment reconciliation for Amazon, Etsy, and Walmart sellers.
Integrates ecommerce sales data across channels for automated accounting sync and payment reconciliation.
Tracks ecommerce profitability by reconciling bank transactions, fees, and payouts from various platforms.
Calculates real-time P&L by automatically reconciling ecommerce sales, costs, and payment gateway data.
Centralizes order and inventory data from ecommerce platforms for accurate financial reporting and reconciliation.
Cloud-based platform for automating payment, bank, and account reconciliation suitable for ecommerce operations.
A2X
specializedAutomates reconciliation of Amazon and Shopify seller payouts directly to accounting software like Xero and QuickBooks.
Automated payout summaries that intelligently group thousands of transactions into 10-20 reconciled accounting line items per deposit.
A2X is a premier ecommerce payment reconciliation software that automates the transformation of complex payout files from platforms like Amazon, Shopify, Stripe, eBay, and Walmart into clean, summarized accounting transactions. It categorizes sales, fees, refunds, taxes, and promotions into reconciled journal entries ready for direct import into QuickBooks, Xero, Sage Intacct, and other ERP systems. This eliminates manual spreadsheet work, ensures 100% payout reconciliation, and provides detailed audit trails for compliance.
Pros
- Seamless integrations with 20+ ecommerce platforms and major accounting software for effortless data flow
- Automated summary journals achieve perfect reconciliation with zero manual intervention
- Robust reporting, multi-currency support, and VAT/GST handling tailored for global sellers
Cons
- Pricing scales steeply with transaction volume, potentially costly for very high-volume enterprises
- Primarily focused on ecommerce marketplaces, less ideal for non-platform payment processors
- Initial setup requires connecting accounts, which may involve a short learning curve for custom rules
Best For
Mid-to-large ecommerce sellers on Amazon, Shopify, or multi-channel platforms needing automated, accurate reconciliation of marketplace payouts.
Pricing
Starts at $19/month (Scale plan, up to 200 orders) scaling to $599/month (Enterprise, 50,000+ orders); custom pricing for larger volumes with annual discounts.
Link My Books
specializedSyncs and reconciles sales and payments from Shopify, Amazon, Etsy, and more to Xero or QuickBooks Online.
Automatic handling and categorization of complex payment gateway fees and adjustments for perfect bank feeds.
Link My Books is an automated reconciliation tool tailored for ecommerce businesses, seamlessly integrating with platforms like Shopify, Amazon, Etsy, Stripe, PayPal, and more to pull sales, fees, refunds, and payout data. It categorizes transactions accurately and syncs them directly into Xero or QuickBooks, eliminating manual bank reconciliation. This ensures precise financial reporting and compliance without spreadsheets or errors.
Pros
- Extensive integrations with 20+ ecommerce and payment platforms
- Fully automated categorization of fees, taxes, refunds, and charges
- One-click bank reconciliation saving hours weekly
Cons
- Limited to Xero and QuickBooks integrations only
- Pricing scales steeply with order volume for high-volume sellers
- No native mobile app or advanced custom reporting
Best For
Ecommerce sellers on Shopify or Amazon using Xero or QuickBooks who need automated multi-channel payment reconciliation.
Pricing
Starts at $19/month for up to 200 orders, scaling to $199+/month for 10,000+ orders; 14-day free trial.
Synder
specializedAutomatically syncs ecommerce transactions from multiple platforms to QuickBooks or Xero for seamless bank reconciliation.
Smart auto-matching engine that learns and applies custom reconciliation rules across diverse payment types and currencies
Synder is an automated payment reconciliation platform tailored for ecommerce businesses, seamlessly integrating with processors like Stripe, PayPal, Square, and Authorize.net to sync transactions into accounting software such as QuickBooks Online, Xero, and FreshBooks. It automates the matching of payouts, fees, refunds, and taxes, handling multi-currency and multi-channel complexities to ensure accurate financial records. By reducing manual data entry, Synder minimizes errors and streamlines bookkeeping for online sellers.
Pros
- Robust integrations with 20+ payment gateways and major accounting platforms
- Intelligent auto-reconciliation rules for complex transactions like fees and refunds
- Real-time syncing and customizable reports for better financial insights
Cons
- Pricing tiers scale steeply with transaction volume, limiting affordability for high-volume users
- Initial setup and rule configuration can require some technical familiarity
- Free plan caps at 50 transactions/month, insufficient for most growing ecommerce stores
Best For
Mid-sized ecommerce merchants processing payments across multiple gateways who need automated reconciliation into QuickBooks or Xero.
Pricing
Free for up to 50 transactions/month; Pro at $39/month (500 transactions); Business at $99/month (5,000 transactions); Enterprise custom pricing.
PayTraqer
specializedProvides automated daily reconciliation of Shopify payments, fees, refunds, and taxes to accounting software.
3-way reconciliation engine that matches orders, payments, and fulfillment data with AI-driven discrepancy detection.
PayTraqer is an automated payment reconciliation software tailored for e-commerce businesses, enabling seamless matching of transactions across platforms like Shopify, WooCommerce, BigCommerce, and gateways such as Stripe, PayPal, and Authorize.net. It automates the reconciliation process by comparing orders, payments, and payouts, flagging discrepancies, and generating detailed financial reports. The tool supports multi-currency handling and provides real-time insights to streamline accounting workflows and reduce manual errors.
Pros
- Robust integrations with 20+ e-commerce platforms and payment gateways
- High-accuracy automated matching including fees, refunds, and chargebacks
- Customizable dashboards and exportable reports for compliance and audits
Cons
- Pricing scales quickly with transaction volume, less ideal for very small stores
- Occasional delays in data syncing during peak periods
- Advanced customization requires some technical setup
Best For
Mid-sized e-commerce merchants processing thousands of transactions monthly who need reliable automation without a steep learning curve.
Pricing
Starts at $49/month for up to 1,000 transactions, $99/month for 5,000, with enterprise plans at custom pricing based on volume.
Finaloop
specializedAutomates end-to-end bookkeeping and payment reconciliation for Amazon, Etsy, and Walmart sellers.
AI-powered 3-way matching that guarantees 100% reconciliation accuracy across all channels and currencies
Finaloop is an automated financial operations platform tailored for e-commerce brands, specializing in reconciling payments from multiple sales channels like Amazon, Shopify, Walmart, and TikTok Shop. It handles complex transactions including sales, fees, refunds, taxes, and reserves, providing 100% accurate financial data in real-time. The software integrates with accounting systems such as QuickBooks, Xero, and NetSuite to streamline bookkeeping and eliminate manual reconciliation efforts.
Pros
- Comprehensive multi-channel reconciliation with 100+ integrations
- Real-time dashboards and automated reporting for accurate P&L
- Strong accounting software connectivity reducing manual work
Cons
- Pricing scales quickly for larger brands, less ideal for startups
- Setup requires initial data mapping which can take time
- Limited customization for non-e-commerce businesses
Best For
Mid-sized e-commerce brands managing sales across multiple marketplaces who need precise, automated payment reconciliation.
Pricing
Custom plans starting at $499/month for up to $100k monthly revenue, scaling to enterprise tiers based on GMV.
Webgility
enterpriseIntegrates ecommerce sales data across channels for automated accounting sync and payment reconciliation.
Multi-channel payment consolidation that auto-maps and reconciles deposits from diverse gateways directly into accounting ledgers
Webgility is a robust e-commerce integration platform that automates order, inventory, and payment synchronization across 100+ sales channels, marketplaces, and accounting systems like QuickBooks and Xero. For payment reconciliation, it matches multi-gateway deposits (e.g., Stripe, PayPal, Amazon Pay) to sales orders, streamlining bank reconciliation and reducing manual data entry. It provides real-time financial visibility, helping businesses manage cash flow accurately across channels.
Pros
- Extensive integrations with 100+ e-commerce and accounting platforms
- Automated payment deposit matching and reconciliation across channels
- Real-time sync reduces errors and manual accounting work
Cons
- Initial setup requires technical configuration and can be time-consuming
- Pricing scales quickly for multi-channel users, less ideal for solos
- More focused on full e-com ops than pure payment reconciliation tools
Best For
Multi-channel e-commerce businesses managing sales on Shopify, Amazon, Walmart, and others that need integrated payment and inventory reconciliation.
Pricing
Plans start at $99/month (Connect), up to $499+/month (Advanced/Enterprise) based on orders and channels; custom quotes available.
TrueProfit
specializedTracks ecommerce profitability by reconciling bank transactions, fees, and payouts from various platforms.
Precision payout reconciliation engine that auto-matches every transaction, fee, and adjustment for pixel-perfect profit accuracy
TrueProfit is a specialized financial automation tool for Shopify merchants that excels in ecommerce payment reconciliation by automatically matching payouts from gateways like Stripe, PayPal, and Shopify Payments to orders. It calculates true profits by deducting all fees, refunds, chargebacks, and expenses in real-time, while providing detailed P&L statements, forecasting, and tax reports. The software integrates with accounting platforms like QuickBooks and Xero to streamline bookkeeping and eliminate manual reconciliation errors.
Pros
- Seamless automated reconciliation of payouts with fees, refunds, and chargebacks
- Real-time profit dashboards and forecasting for quick decision-making
- Native Shopify integration with easy setup and robust accounting exports
Cons
- Limited to Shopify ecosystem, less ideal for multi-platform stores
- Higher-tier plans needed for advanced analytics and unlimited data
- Occasional delays in processing very high-volume transactions
Best For
Shopify store owners focused on accurate payment reconciliation and profit tracking without complex manual accounting.
Pricing
Starts at $29/month (Basic, up to 500 orders), $99/month (Pro, up to 5k orders), $199/month (Enterprise, unlimited); 14-day free trial available.
BeProfit
specializedCalculates real-time P&L by automatically reconciling ecommerce sales, costs, and payment gateway data.
Automatic reconciliation of multi-currency transactions and marketplace fees across 100+ integrations for precise net profit tracking
BeProfit is an e-commerce profit analytics platform that specializes in payment reconciliation by automatically syncing data from sales channels like Shopify, Amazon, and payment gateways such as Stripe and PayPal. It calculates true profits by reconciling transactions against fees, refunds, taxes, shipping costs, and COGS, providing detailed P&L reports and dashboards. The tool helps merchants identify discrepancies, optimize margins, and make data-driven decisions without manual spreadsheets.
Pros
- Multi-channel integration for seamless data syncing and reconciliation
- Accurate profit calculations including all fees, taxes, and refunds
- Customizable dashboards and real-time analytics for quick insights
Cons
- Limited advanced customization for very complex operations
- Steep initial setup for businesses with high transaction volumes
- Reporting exports could be more flexible
Best For
Mid-sized e-commerce businesses with multiple sales channels needing automated profit reconciliation and analytics.
Pricing
Starts at $29/month (Starter, up to 500 orders) scaling to $299/month (Enterprise, unlimited), with annual billing discounts.
Pipe17
enterpriseCentralizes order and inventory data from ecommerce platforms for accurate financial reporting and reconciliation.
Universal API connector enabling seamless, real-time data flow across disparate ecommerce ecosystems without custom coding.
Pipe17 is a middleware platform that connects ecommerce sales channels like Shopify, Amazon, and Walmart with fulfillment providers, ERPs, and other backend systems for automated order routing and inventory sync. For payment reconciliation, it provides real-time syncing of order and basic payment data from multiple channels, offering visibility into transaction statuses and payouts. However, it lacks specialized tools for advanced matching, fee breakdowns, or bank statement reconciliation, positioning it more as an operational integrator than a dedicated finance solution.
Pros
- Extensive no-code integrations with 200+ apps including major sales channels and payment gateways
- Real-time data sync reduces manual reconciliation efforts for basic payment tracking
- Scalable for high-volume multi-channel operations
Cons
- Limited native support for advanced payment reconciliation like fee calculations or bank matching
- Pricing is enterprise-level and may not justify use solely for reconciliation
- Focuses more on fulfillment and inventory than deep financial reporting
Best For
Multi-channel ecommerce merchants needing integrated order and basic payment sync alongside fulfillment automation.
Pricing
Custom quote-based pricing scaling with order volume and integrations; typically starts at $500-$1,000/month for mid-sized operations.
ReconArt
enterpriseCloud-based platform for automating payment, bank, and account reconciliation suitable for ecommerce operations.
AI-powered transaction matching that self-optimizes rules for 99% straight-through reconciliation rates
ReconArt is a cloud-based automation platform specializing in account reconciliation, transaction matching, and financial close processes for high-volume data. For ecommerce payment reconciliation, it automates matching of payments from gateways like Stripe, PayPal, and Adyen against sales orders, handling fees, refunds, chargebacks, and multi-currency transactions. Its AI-powered engine learns from user rules to achieve high straight-through processing rates, reducing manual effort significantly.
Pros
- AI-driven auto-matching with 95%+ accuracy for high-volume ecommerce payments
- Scalable for unlimited transactions and multi-entity support
- Robust integrations with 100+ data sources including major payment processors
Cons
- Steep initial setup and configuration for non-finance users
- Lacks native ecommerce-specific dashboards or order management views
- Enterprise pricing may be prohibitive for small businesses
Best For
Mid-to-large ecommerce operations with complex, high-volume payment streams needing automated reconciliation.
Pricing
Quote-based subscription starting at around $5,000/year for basic plans, scaling with transaction volume and users.
Conclusion
The 10 tools reviewed represent top solutions for ecommerce payment reconciliation, with A2X emerging as the standout choice—particularly adept at automating Amazon and Shopify payout alignment with accounting software. Link My Books impresses with its broad support for multiple platforms including Etsy, while Synder excels in syncing diverse transactions for seamless bank reconciliation. Each tool caters to specific needs, but A2X’s focus on core platform integration makes it the most versatile.
To simplify your payment reconciliation process, start with A2X for efficient, automated tracking of key sales channels. If your focus is on multi-platform support or transaction detail, explore Link My Books or Synder to find the best fit for your business.
Tools Reviewed
All tools were independently evaluated for this comparison