5 Best Ecommerce Payment Reconciliation Software In 2025

Most sellers assume manual accounting is enough to reconcile payments. But when dealing with 1000s of transactions, can spreadsheets alone cut it? 

Accurate reconciliation helps you protect your bottom line and is important for the financial integrity of your business. And using manual means to match your sales and bank records simply isn’t enough. You will set yourself up for inconsistent records, slow transaction mapping, and even slower payment processing to creep through—leaving you to deal with revenue leakages and operational inefficiency in return.

Here’s where an ecommerce payment reconciliation software can help.

It not only reduces payment processing and reconciliation to minute-long tasks. But it also gives you a bird’s eye view of your overall profitability and financial health to make better, data-informed decisions.

Before we list the best software options, let’s unpack what makes payment reconciliation a pressing pain for sellers and financial managers.

What Makes Ecommerce Payment Reconciliation a Challenge for the Sellers?

Processing the sheer volume of orders and payments is hard enough. But ecommerce sellers also have to deal with the following challenges:

• Managing sales records across multiple marketplaces and payment channels: Even if you have the technology to manage bookkeeping and reconcile your finances, only a few ecommerce payment reconciliation software are compatible with every ecommerce marketplace.  Without a single platform to consolidate these records, the risk of data inconsistencies increases, making accurate reporting more challenging and time-consuming.
• Managing a huge volume of transactions: Accurately mapping and recording the massive, diverse set of financial data isn’t easy, especially if you rely on manual accounting since there’s a higher chance of error.
• Maintaining accurate records: From marketplace fees to invoices to tax deductions, you need to account for multiple transactions across multiple payment gateways to accurately reconcile financial records. This is often hard to achieve with manual data entry and matching.
• Navigating the complicated fee structure of marketplaces: Say you are selling on Amazon and eBay. Each of these platforms charge different commissions, shipping charges, and in the case of Amazon, FBA (Fulfilled by Amazon) warehousing costs, all of which are deducted from your earnings. Reconciling invoices across these marketplaces is never smooth sailing. 
• Human errors in manual reconciliation: Adding line items to a spreadsheet sounds simple on paper. However, manual payment reconciliation becomes a time-consuming, error-prone process due to the complexity of transactions (refunds, billing inconsistency, overcharges, etc.) and the differences in payment timelines.
• Identifying and preventing fraudulent transactions and record mismatch: It takes tremendous precision and effort to effectively flag and correct accounting errors, especially for discounts, refunds, and credit-related issues.
• Handling chargebacks, refunds, and disputes: Reconciling chargebacks and refunds to the original sale while accounting for the marketplace deductions is often challenging due to timing mismatches. As a result of this delay, the reconciliation and book closing process takes longer. 

What Features Make the Best Ecommerce Payment Reconciliation Software?

Now, not every payment reconciliation software is created equal. To make sure you’re choosing the right one, look at whether or not the software supports the following features:

• Automation capabilities for reconciliation, inventory management, and reporting: Having the ability to automate transaction mapping and accounting should be the bare minimum. It should automatically collect, process, compare, and reconcile data points across sales channels and platforms.
• Multi-channel integration: Ecommerce reconciliation software that integrates multiple sales channels and platforms into a unified system makes payment reconciliation less stressful. It can smoothly bring together bytes and bytes of siloed financial data generated across marketplaces using different modes of payment.
• Real-time reporting and analytics: Look for financial reporting and business analytics features that can help you keep tabs on performance at the channel or SKU level. It should build you actionable revenue reports and forecasts to optimize costs and save on expenses.
• Scalability and customization: From the ability to process a high volume of transactions to integrating new sales channels to advanced data mapping and analytics, the ideal payment reconciliation software will help you scale and sell more.

Best Ecommerce Payment Reconciliation Software at a Glance

Here’s a summary of the best e-commerce reconciliation solutions in the market.

5 Best Ecommerce Payment Reconciliation Software in 2025

Here are five of the best ecommerce payment reconciliation software.

1. Webgility

Webgility is more than just your ecommerce reconciliation software -  it’s the trusted choice for over 20,000 brands as an all-in-one ecommerce automation software. With Webgility, you can connect your accounting solutions, like QuickBooks and NetSuite, which contain your banking records, to your marketplaces, platforms, and POS. 

Webgility automatically matches your net income - payments, fees, and refunds - from sales with the corresponding bank deposits. It helps you identify discrepancies, such as missing transactions or incorrect amounts and highlights them for review. You can review any discrepancies flagged by Webgility. The platform provides detailed reports and insights, allowing you to investigate any issues. 

Unlike other solutions, Webgility is tailored for sellers managing multiple online stores and marketplaces. It automates not just payment reconciliation but also order processing, inventory management, and financial reporting, all through one central dashboard.

User review

Automated real-time accounting

Accurately sync, process, and account for revenue, profit, loss, and tax liability across jurisdictions.

Your sales transactions are updated on Quickbooks in real-time. With fully automated workflows, you save 10+ hours weekly on manual bookkeeping. You can fetch data, manage listings, and forecast inventory needs on command, reducing stress and keeping records updated in real time.

Seamless integration across sales channels

Webgility integrates with 60+ platforms, including eBay, Etsy, Amazon, and other leading platforms, to centralize ecommerce management. This makes mapping and processing transactions and payouts across sales channels as simple as clicking a button. For example, Webgility will reconcile Amazon-originated journal entries only after receiving the settlement report from Amazon. 

Timely refund and dispute management and inventory synchronization

With Webgility, you can easily track refunds, partial refunds, chargebacks, and disputes automatically. And the inventory is updated with every return in real time. This takes inventory level management from 0 to 1 in no time.

You also get greater control over your product catalogs with advanced inventory reporting and alerts, making stock management much easier and more efficient.

Detailed payment reconciliation reports and insights

You get a 360-degree view of all your financial data in one place. Webgility makes detailed records of sales, discounts, fees, refunds, chargebacks, sales tax, and more for every sales channel when generating payment reconciliation reports. This level of granular insights will help you stay on top of your financial operations.

Pricing

Webgility’s basic plan starts at $49/month and its Pro plan starts at $99/month. Check out our full pricing here.

Click here to take a product tour of Webgility. No sign-up is needed.

2. Bookkeep

Bookkeep is often recommended for its accrual-based accounting capabilities while offering a “set it and forget it” ease of use.

Bookkeep is best suited for ecommerce sellers who need accurate, real-time financial reporting across multiple platforms without manual intervention. With Bookkeep’s accrual-based accounting, you get daily email reports that compile thousands of transactions from your ecommerce platforms, giving you real-time insights into your sales, fees, and profits.

Standout features

• Daily summary emails compiling 1000s of individual orders into clean financial summaries. This keeps you updated on channel-level performance.
• Daily accrual-based summaries and deposits, which make it easier to match transactions and reconcile account balances
• Integrates with 60+ ecommerce platforms and POS systems, allowing you to pull and consolidate data in one place.

Pricing

Bookkeep offers revenue-based pricing, starting at $60/month or $50/month if you get the annual plan.

3. Finaloop

Finaloop combines AI and in-house experts to offer real-time bookkeeping with a dedicated team of accountants. This negates the need for you to purchase a tech stack to manage your ecommerce payment operations. 

With integrations to multiple ecommerce platforms and payment systems, Finaloop automatically syncs your financial data and delivers it to your accounting software, making it the perfect choice for growing ecommerce businesses that need expert financial management at every step.

Standout features

• Proprietary software for full bookkeeping, which connects with multiple platforms and payment systems to automatically sync and organize all your financial data within a smart dashboard
• Real-time financial reconciliation with 100% accuracy. Since CPAs and bookkeepers overlook the accounting process enabled by technology, you get 24/7 data sync to manage day-to-day operations well
• Simplified planning for federal income tax. You get tax-ready books and specialized guidance for tax planning, including how to optimize for deductions and file the tax return

Pricing

Finaloop, too, charges based on revenue. Their pricing plans start at $65/month (or $59/month for annual plans) for a company generating $1K - $100K in annual revenue.

4. MyWorks

MyWorks provides direct connection integrations to Shopify and Woocommerce store owners, allowing them to integrate with QuickBooks and Xero at a deeper level.

It takes away the hassle of toggling between platforms by letting you manage the store’s finances from within the ecommerce platform.

Standout features

• Automate syncing and transferring of orders, inventory, and product data in real time. This saves your hours on manual data entry and reduces human error
• Customize how your data syncs across platforms. You can sync data at preferred intervals, such as after every 5, 10, 30, or 60 minutes
• Flexible mapping for product and customer data. You can decide how MyWorks maps data based on category or product level
• Intuitive and simple interface makes software implementation buttery-smooth

Pricing

MyWorks has feature-based and platform-specific pricing plans. You will have to pick between Woocommerce/Shopify and QuickBooks Online, Desktop, POS, and Xero for integration.

Paid plans start at $24/month ($19/month for annual plans).

5. Synder

Synder is an all-in-one accounting automation software for teams dealing with complex operations and multisource data.

It can help you synchronize data from ecommerce platforms to QuickBooks Online, QuickBooks Desktop, Xero and Sage Intacct while automating transaction syncing, reconciling, and reporting across sales channels.

Standout features

• Import, categorize, and sync sales transaction data across 30+ platforms with seamless integrations and customizable workflows 
• Choose from two types of sync modes: ‘Summary’ and ‘Per Transaction’
• Record taxes withheld by different marketplaces and calculate your liabilities without surprises later 
• Prioritize data security with SOC2 compliance and industry-standard encryption protocols. It also complies with HIPAA, GDPR, and CCPA regulations

Pricing

Synder provides four different pricing plans based on the order volume, starting at $65/month or $52/month for the annual plan. You can also tour its features with a 15-day free trial.

How to Choose the Best Ecommerce Payment Reconciliation Software?

Beyond the four essential features we covered earlier—automation, integration, analytics, and scalability—look for software with features that can improve and optimize your overall ecommerce operations. For example:

• Automated import and syncing of data to eliminate manual data entry. Capturing and syncing sales data, including marketplace fees, refunds, payouts, and more, is a crucial step in payment reconciliation. If the software automates the process, you can save admin work and avoid human oversight for more accurate accounting.
• Factor in the speed and accuracy of transaction mapping and accounting. This is because some payment reconciliation software can compute the financial data within minutes, while others may take longer, especially if you’re processing larger volumes of data daily.
• Look for AI-enabled features to improve operational efficiency. You should be able to build intelligent workflows and carry out tasks on command—whether it’s fetching order details, syncing inventory across channels, or calculating sales tax liabilities. This lets you achieve speed and consistency to get ahead of the competition
• Pay special attention to the ease of use. No matter how effective the software is, if it has a clunky interface, you end up spending more time and resources training the staff than actualizing its benefits. It should ideally accommodate users with varying levels of accounting experience.
• Customer onboarding support is another factor to consider. Every software comes with a learning curve, including payment reconciliation software. Pay closer attention to how much onboarding and IT support the vendor offers to implement the software faster

Finally, consider the credibility of the software vendor. This will ensure you have a smooth partnership over the long haul. But in any case, perform due diligence to shortlist, trial, and select the right software for your business needs.

Get The Webgility Advantage: Automate Accounting and Save Hours on Manual Data Entry

Investing in payment reconciliation software pays off in time and cost savings wasted on manual data entry. You can spot and plug revenue leakages, cut down expenses, and improve business growth in a fast yet sustainable manner.

However, software selection can be a real pain. Especially with the research and decision fatigue right in tow.

But if there’s one software solution that ticks all the must-have functionalities, it’s Webgility. We may be biased, but the 20,000+ customers we support will tell you otherwise. Webgility is fast and flexible and offers powerful automation for accounting and reconciling payments across marketplaces and POS systems.

Click here to tour its features with a 15-day free trial. Or book a meeting slot to get a one-on-one demo.

FAQs

1. How many integrations should the software support?

If you’re growing fast or aiming to scale, go for the solution offering a maximum number of integrations, say 60 or above, so you’ll always have the architecture to support complex operations.

2. What are some add-on features to consider when choosing the software?

To get the best ROI, choose ecommerce payment reconciliation software offering add-on features like automated data matching and categorization, compliance with security regulations, fraud detection, mobile accessibility, and API.