June 4, 2024
10 min

5 Top E-commerce Payment Reconciliation Software [Expert Picks]

Boost your online store’s success with the best E-commerce payment reconciliation software. Learn how to choose the right one for your business.
5 Top E-commerce Payment Reconciliation Software [Expert Picks]
Table of contents

Since an e-commerce business receives payments from different sources, it's easy to have inaccurate financial records because of incorrect transaction details. 

The need to comply with different standards means inaccuracy and inefficiency don't belong in your online business, which makes manual reconciliation something to avoid. 

The better option is to use e-commerce payment reconciliation software to automate the process and minimize errors and discrepancies that may cost you loads of money.

Key Takeaways from this Post

Automating Payment Reconciliation: E-commerce payment reconciliation software reduces errors, saves time and money, and enhances customer satisfaction by ensuring accurate financial records and efficient payment processing.
Top Software Options: Recommended tools include Link My Books, Taxilla, Stripe, eVanik, and Vinculum, each offering features like financial analytics, multi-channel integrations, and real-time data syncing.
Key Features to Consider: Important features for reconciliation software are customizability, integration capabilities, user-friendliness, security, scalability, and real-time data syncing to streamline financial management across sales and payment channels.
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TL;DR - 5 Top E-commerce Payment Reconciliation Software

There are many payment reconciliation software your chosen accountant can use, depending on your needs. 

Here's the quick list that forms the basis of our detailed discussion in an upcoming section:

  1. Link My Books
  2. Taxilla
  3. Stripe
  4. eVanik
  5. Vinculum

Link My Books collects financial data from your sales channels and links it with your Quickbooks or Xero accounting software for smooth payment reconciliation. You can check out our free trial today to see how our tool does all the heavy lifting for you.

Stylish female entrepreneur with a decorative necklace using her laptop at a wooden desk.

What is Payment Reconciliation?

Payment reconciliation is the financial process of ensuring that your business's transaction records match correctly with payment data from services such as Shopify Payments, bank accounts, PayPal, and more.

Online payment reconciliation ensures the transactions in your chosen e-commerce accounting software record the correct amounts of money your business receives or pays out. 

If you record your transactions manually in ledgers, these monetary amounts should also match. 

Besides matching the actual money transactions, payment reconciliation captures other transaction data such as:

  • Dates of the transactions
  • Invoices
  • Payment receipts
  • Payment methods
  • Bank statements. 

E-commerce payment reconciliation is a vital part of e-commerce accounting, and you should do it at least once a week. If you are really held up, at least once a month will do. 

Hands of a person calculating numbers on a calculator over financial documents.

Benefits of Using Payment Reconciliation Software

There are many advantages to reconciling your payments using reconciliation software. 

Here are some of the main benefits:

Keeping Accurate Financial Records

The advanced algorithms in e-commerce reconciliation software minimize the risk of errors and discrepancies. Reducing the risk can save you money. 

For example, you won't have to pay any fines because you won't have any tax underpayments. 

Automation Saves Time and Money

With payment reconciliation software, you'll only spend about 10 minutes transferring data from your bookkeeping software to your accounting software. 

Additionally, you'll save money because the manual labor for reconciling your payment details will be reduced significantly.

Enhanced Customer Satisfaction 

Every customer wants to pay for goods and services quickly and efficiently. 

Using reconciliation software helps boost customer satisfaction because you process payments, chargebacks, and refunds precisely and securely. 

Improved Financial Visibility

Payment reconciliation enhances financial visibility because everything happens within the same system, making it easy to collect financial data for accounting and other uses. 

For example, you can see how your cash flows in or out of your business. 

Reconciliation Prevents Revenue Leakages 

E-commerce reconciliation software can help you catch incomplete invoices or payments, thus saving you money you wouldn't have noticed missing. 

Improved Decision-making

Payment reconciliation provides information for decision-making, such as payment efficiency, transaction trends, and customer behavior. 

Aids in Financial Planning 

You can improve your financial planning both in the short and long term. 

Reconciliation software helps you track your e-commerce cash flow to determine your available money for investment, operations, or capital expenses.

Overhead view of hands holding a calculator and writing in a notebook.

Features to Look for in E-commerce Payment Reconciliation Software

There are several excellent e-commerce payment reconciliation software, making it challenging to decide on one. The software you choose will depend on your budget, expected outcomes, and specific needs. 

You'll want to consider the following factors to decide on the best option:

  • Customizability: Can the solution you choose allow you to make changes in report formatting, integrations with other apps, or matching rules?
  • Diverse integrations: Linking your payment reconciliation software with other software increases functionality. It's essential to be able to integrate with your e-commerce platforms and your accounting software. 
  • Technical support: You should easily and quickly access the software’s IT support whenever you need help with technical issues or setting up the software. 
  • Ease-of-use: Does the software have a simple user interface that is easy to learn? There should also be a lot of content, like videos and blog articles, to help you understand the software faster. 
  • Security: You'll want a solution that secures financial information for you and your customers. Look for elaborate data protection, encryption, and control to access. 
  • Scalability: Your e-commerce business is bound to expand. Can the software accommodate this growth and the increased number of transactions?
  • Real-time data syncing: If your chosen software can synchronize data in real time, you can quickly find and address any inaccuracies to prevent losses. 

5 Top E-commerce Payment Reconciliation Software

Here are the five top e-commerce reconciliation software you can use: 

1. Link My Books

Link My Books Homepage

E-commerce businesses, accountants, and bookkeepers use Link My Books to automatically record tax information, sales, fees, and refunds. Our reconciliation platform then sends these data to your accounting software for accurate bookkeeping and accounting. 

Link My Books Features

You can enjoy the following features with Link My Books:

  • Payout reconciliation
  • Financial analytics and strategic insights
  • Link My Books benchmarking
  • COGS and tax calculations
  • Multi-channel integrations

Payout Reconciliation

A screen shot of the connect bookkeeping account.

Link My Books payout reconciliation ensures accuracy and visibility when syncing your transaction data to your accounting software from all the sales channels you use. 

All your payouts are added to your accounting software individually or in bulk using AutoPost, which includes a summary for each transaction. 

Connect with us for a demo and see why Link My Books remains the best automation software for over 8,000 bookkeepers, e-commerce accountants, and e-commerce business owners in the US, Australia, and the UK. 

Financial Analytics and Strategic Insights

A view of a cross channel performance dashboard.

Our financial analytics feature provides a clear view of each channel's performance, all in one central place. 

You can see metrics such as refund ratio, ROI, profit and loss per channel, and sales growth. These metrics are ideal insights for decision-making, such as deciding which channels to double down on for more success. 

Link My Books Benchmarking

A website page with the words no more growing in the dark.

Our Benchmarking allows you to gauge how your business performs based on metrics such as advertising fee ratio, refund ratio trends, fee ratio, and sales growth. 

The insights from the Benchmarking help you grow the business because they make decision-making easier based on data rather than mere personal judgment. 

COGS and Tax Calculations

A screen shot of the profit and loss statement.

Like every business owner, you want profits. Link My Books tracks the cost of goods sold (COGS) to show how profitable your business is. 

Taxes are an integral part of e-commerce; our tool helps you get your taxes right every time.

Our automatic software ensures that each sold item has the correct tax, whether you sell it locally or internationally. You can rest assured that our tax tracking will ensure you don't underpay or overpay taxes. 

Multi-channel Integrations

Multi-channel display

As discussed earlier, your payment reconciliation solution should be compatible with sales channels, payment channels, and bookkeeping and accounting software. 

Link My Books streamlines your processes across payment processors like Klarna, ClearPay, and PayPal. 

The software also streamlines processes across sales channels like Walmart, Amazon, Shopify, Etsy, TikTok Shop, eBay, Square, and WooCommerce. 

Link My Books can sync and transfer transactional data from:

2. Taxilla

Taxilla Homepage

Taxilla is an all-in-one regulatory technology platform for large businesses and enterprises to automate invoicing, compliance, and reporting. 

The platform has features made explicitly for the e-commerce industry, including enReconcile, its payment reconciliation software. 

Taxilla Features

You can enjoy the following features with Taxilla:

  • enReconcile: Taxilla’s enReconcile streamlines your ledger processing, payment processor reconciliation, and order management. 
  • enReport: Taxilla allows you to prepare and file different tax reports based on accurate calculations and automatically generated data. 
  • enInvoice: Taxilla’s enInvoice helps you make and use global invoices that comply with government tax regulations. The feature allows you to convert multiple orders into invoices and convert your metadata from ledgers to invoices to reports. 

3. Stripe

Stripe Homepage

As a global payments handler, Stripe manages online and offline transactions for thousands of businesses. The company's Invoicing software can help you deal with reconciliation across different payment methods. 

Stripe Features

Here are some features you can enjoy with Stripe:

  • Invoicing: Stripe has a robust customization system for invoices. You can add product details, taxes, and customer details. 
  • Analytics: Stripe has analytics and reporting tools for tracking invoices and retrying failed payments automatically. 
  • Automation: With Stripe, you can automatically send out invoices and ensure the payments on your bank statements match the invoices. 

4. eVanik

eVanik Homepage

eVanik is a robust all-in-one platform for e-commerce management needs related to reconciling payments, inventory, returns, and shipping. 

eVanik Features

Here's what you can enjoy with eVanik:

  • Payment reconciliation: eVanik allows you to verify your payments, charges, inventories, and taxes in real time to reduce customer disputes, potential fraud, and critical human errors. 
  • Cross-channel inventory management: With eVanik, you can connect your marketplaces and see real-time stock level updates each time you sell an item. You'll thus be able to make timely stock replenishments based on what items are likely to sell fast to avoid tying down your capital in unmoving inventory. 
  • Amazon marketing: eVanik can automatically reprice your Amazon products in real time to maximize your profits. You can also automatically monitor and manage negative reviews to avoid losing business from potential customers. 

5. Vinculum 

Vinculum Homepage

Vinculum offers multi-channel software solutions such as reconciling payments, managing product information, listing products, and managing warehouses. 

Vin Reco is the company's payment reconciliation software that handles marketplace reconciliations, accounting and GST reports, disputes, and webstore reconciliations. 

Vinculum Features

You can enjoy the features below with Vinculum:

  • Payment reconciliation: Vin Reco is ideal for monitoring financial leakages where you could potentially lose money through overcharged shipping fees and commissions or incomplete transactions. 
  • Inventory management: With Vinculum, you can automatically update your multi-channel inventories in real-time and manage your orders, shipping, and returns. 
  • Product information management: Vinculum helps you manage your catalog by uploading products in bulk to compatible sales channels. You can also standardize your product aspects, such as naming formats, organization, and specifications. 

Frequently Asked Questions (FAQs)

Here are common questions e-commerce accountants and business owners usually ask: 

Can Payment Reconciliation Software Integrate with Existing E-commerce Platforms?

Yes. Payment reconciliation software can integrate with different e-commerce platforms. 

For instance, Link My Books integrates with platforms like Amazon, Shopify, WooCommerce, Etsy, Square, eBay, Walmart, and even TikTok Shop! 

What Types of Payment Methods Can be Reconciled Using This Software?

You can reconcile different types of payment methods with payment reconciliation software, including:

  • Bank transfers
  • Payment gateways such as PayPal, ClearPay, and Shopify Payments
  • Credit cards
  • Debit cards.

Some software even reconcile other digital wallet payments from platforms like Amazon Pay, Square Wallet, Stripe Terminal, and Walmart Pay. 

Are There Automated Solutions for E-commerce Payment Reconciliation?

Yes, there are automated solutions for e-commerce payment reconciliation. Each software is actually highly automated. 

However, you still have to perform functions such as analyzing and interpreting data, analyzing key performance indicators, setting and activating your internal controls, and monitoring the software's progress weekly or monthly. 


With the right e-commerce payment reconciliation software, you can automate your e-commerce accounting within minutes. Automation makes it easy to reduce errors, discover potential issues, and correct them promptly. 

Link My Books is the best payment reconciliation software for saving you hundreds of hours of manual work per month. 

Grab our 14-day free trial to see how we can help you reconcile e-commerce payments and save time and money!

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