Best eCommerce Payment Reconciliation Software 2025

By 2027, the global ecommerce market is expected to generate $5.5 trillion. As a player in the ecommerce space, you know that is an outcome of countless transactions, all of which must be properly tracked and accounted for. 

Ecommerce payment reconciliation software is a must-have solution for any business that wants to maintain adequate control over its finances. 

Let’s take a look at what payment reconciliation software can do, as well as review the best ecommerce payment reconciliation software to choose from. 

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What is eCommerce Payment Reconciliation?

Before we dive into the helpful software, it’s useful to define what ecommerce payment reconciliation is. As part of an ecommerce company’s financial processes, ecommerce payment reconciliation verifies transaction records with payment data from banks, financial institutions, and payment gateways. 

As you can imagine, the larger the volume of transactions and payment processors, the more difficult it is to keep track of manually. 

Payment reconciliation software like SolveXia automates the process of reconciliation by performing transaction matching without the need of human intervention. The software connects with your various sources of data to centralize and streamline the critical workflow with total accuracy. 

What is Payment Settlement?

As the first step in processing a payment, a payment settlement must take place. A payment settlement happens when money is transferred between accounts in order to complete a payment. Only then can reconciliation be executed to verify that the amount was correct. 

What is Payment Reconciliation?

After payment settlements have occurred, payment reconciliation compares payment details within an accounting system with the amount that was transferred (paid). 

The goal is to make sure that the amounts and information is in alignment with one another. If not, investigations must be carried out so that adjustments can be made. 

What are the Most Common Payment Reconciliation Problems?

Dealing with payment reconciliation should ideally be a smooth and clear process, but oftentimes, it is filled with challenges. Some of the most common problems that arise include:

• Missing Transactions: In some cases, sellers may skip over recording transactions. As a result, their financial statements and bank statements won’t match up because of the missing information. Rather than manually recording transactions, it’s helpful to leverage accounting automation software that can automatically track transactions.
  
  
• Errors of Reversal: Errors of reversal take place when debits are recorded as credits and vice versa. It’s hard to notice these errors when manually reviewing a large volume of transactions. 

• Lack of Consistency: To reduce issues in the short-term and long-term, it’s best to perform ecommerce payment reconciliation consistently. However, many businesses can’t seem to find the time to do so. That’s why the aid of ecommerce payment reconciliation software can alleviate the burden as it automates every step of the way, thereby saving time, increasing accuracy, and freeing your team’s time to focus on value-add responsibilities. 

• Manual Reconciliation: Manual reconciliation is inevitably error-prone and time-consuming. Automation software is the perfect solution to implement to overcome this major concern. 

How Does eCommerce Reconciliation Work?

Ecommerce payment reconciliation follows the same basic steps as other types of reconciliation, such as account reconciliation and bank reconciliation, to name a few. 

To exemplify what this looks like in practice, here’s an outline of the steps:

1. Data Collection

In order to compare documents and data, you must first have the information in hand. When using multiple payment processors, systems, and spreadsheets (like Amazon, ebay, Stripe, Worldpay etc), this can end up taking a lot of time to compile. 

Instead, with ecommerce payment reconciliation software, solutions like SolveXia can connect all your information systems to centralize data in a secure and accessible location.  

2. Transaction Matching

With all the documentation ready to go, it’s time to match transactions from your ecommerce platform to your other sources of information, such as a payment gateway or bank statement. 

You’ll want to make sure that the transaction amount, date, and vital details are the same across all sources. It’s also important to match these transactions with your internal records. If you have a high volume of low value transactions, an automation tool can reconcile these in seconds instead of days.

3. Discrepancy Identification

Should you find any errors, be sure to highlight them so you can investigate their reasoning. Sometimes, there are explainable causes, such as timing delays or fees. Other times, it may be an indicator of fraud or a bigger problem. 

4. Resolution

Once you’ve discovered the reason for the discrepancy, you can take action to resolve it and/or update your own records. 

5. Reporting

At the end of the process, it’s best to create a report of everything that was done to share with relevant parties and stakeholders. eCommerce Payment Reconciliation Software like SolveXia can do this automatically. 

What is the Best eCommerce Payment Reconciliation Software?

If you’re looking to automate the entire workflow above, you’re in the right place as we are going to share some of our favorite ecommerce payment reconciliation software options. 

1. SolveXia

SolveXia is a low-code platform that automates spreadsheet-driven data preparation and manual processes for finance and accounting teams. 

Features:

• Complex matching rules for reconciliation 
• Integrates with existing systems 
• Automated and customizable reports and dashboards
• Easy-to-use interface with drag-and-drop functionality 
• Automates key finance functions, i.e.: expense management, regulatory reporting, revenue management, process optimization, and more 

Pros:

• Works with any type of data 
• Cloud-based and accessible 
• Data transformation and enrichment capabilities
• Scalable 

2. Stripe

Stripe is a global payments handler that offers features like:

• Invoicing
• Analytics
• Automation 

Pros:

• User-friendly interface 
• Good customer support 

Cons:

• Lack of customization capabilities
• Difficulties dealing with mixed billing periods for subscriptions 

3. Finaloop

Finaloop is an ecommerce accounting software with real-time bookkeeping. 

Features:

• Real-time bookkeeping
• Tax administration with e-filing 
• Integration with existing systems 

Pros:

• Cash flow projections
• Tax preparation 
• Ongoing support 
• Automated reconciliation 

Cons: 

• Lacks inventory management 
• Can’t mark off transactions that have been reviewed already 

4. Taxilla

Taxilla is a regulatory technology platform that is designed for enterprises. 

Features: 

• Automated reconciliation 
• Invoicing 
• Audit trails 

Pros:

• Secure and collaborative environment 
• Integrates with existing systems 
• Multi-currency support 

Cons: 

• Focused on enterprises
  

5. Vinculum 

Vinculum is an AWS cloud-based payment reconciliation software. 

Features:

• Payment reconciliation 
• Inventory management 
• Product information management 

Pros:

• Scalable 
• Multi-currency support 
• Fraud detection 

Cons:

• Inventory allocation issues 
• Steep learning curve 

How to Choose the Best eCommerce Payment Reconciliation Software?

Having taken a look at some of the best ecommerce payment reconciliation software in the market, you may be wondering how to choose what’s best for your business. 

Here are some considerations to keep in mind: 

• Ease-of-Use: You’ll want a software that is easy to use for every level of technical ability. Since not everyone knows how to code or wants to rely on IT team support, you can look for payment reconciliation software like SolveXia that is intuitive and offers drag-and-drop functionality to design your own workflows (without any IT team required).
  
  
• Integrations: The best reconciliation software can integrate with your other existing systems, such as your CRM and accounting software.
  
  
• Support: No matter how easy the platform is to use, you’ll want the option to get in touch with customer support and have access to useful resources.
  
  
• Security: Given the sensitive data at play, security is a top priority. Seek solutions that have encryption and bank-grade security measures with constant updates. 

What are Best Practice Tips for Payment Reconciliation?

To protect the accuracy of your financial statements and integrity of transactions, payment reconciliation best practices should be put into place. These include:

• Automation: Hopefully, your transaction volume will only continue to increase. With increasing transaction volume and payment processors, it becomes more and more difficult to keep up manually. Automation software should be used to streamline the process with full accuracy and ease.
  
  
• Clear policies: Set clear policies and processes for reconciliation so everyone knows what is expected of them and what to do in the event of a discrepancy. 

• Regularity: Ecommerce transactions move fast, so should ecommerce payment reconciliation. It’s important to conduct it on a consistent basis as it will help with decision-making capabilities and to reduce issues. 

• ‍Reporting: Detailed reconciliation reports help management and supervisors to understand what actions took place.

Why Invoice Reconciliation is Important?

Invoice reconciliation, or payment reconciliation, is so valuable to ecommerce businesses because it impacts:

• Financial Accuracy: Accurate accounts are of top priority for any business to generate financial statements with integrity and make informed business decisions. Reconciliation ensures the accuracy of accounts and statements.
  
  
• Compliance: Businesses must uphold accounting standards, and payment reconciliation helps to make sure that everything is in good order.
  
  
• Cash Flow Management: The inflow and outflow of funds allows businesses to know what is available to cover expenses and for financial planning. Invoice reconciliation enables businesses to keep an eye on cash flow.
  
  
• Customer Satisfaction: While it’s not commonly thought of as a main benefit of invoice reconciliation, customer satisfaction is definitely a benefit. This is because with  e-commerce reconciliation, companies can ensure that transactions are being properly and securely executed, which protects customers’ interests. 

What are Use Cases for eCommerce Payment Reconciliation Software?

Ecommerce payment reconciliation software is a must-have for any ecommerce business, but it proves especially valuable in use cases that would otherwise cause confusion, like:

1. Overcharged Orders

No one wants to be overcharged, but it can happen. Payment reconciliation can bring this to a seller’s attention to rectify it in a timely manner. 

2. Unpaid Orders

Reconciliation software will notify you of unpaid orders so you can collect what you are rightfully owed in a timely manner. 

3. Overcharged Returns

Reconciliation software will also protect sellers against overcharged returns. 

All in all, the goal of ecommerce payment reconciliation is to protect your profitability, oversee cash flow management, and ensure that financial statements are always up-to-date and accurately reflected. 

Since financial health dictates every business decision you’ll make, you’ll want to remain confident that the information you have in hand is right. 

The Bottom Line 

The world of ecommerce is fast-paced, and so are the finances that come along with it. Manual efforts are no longer going to cut it. Ecommerce payment reconciliation software will save your business time and money by automating the process, connecting various data systems, and reducing mistakes. 

If you’re ready to see how a payment reconciliation tool like SolveXia can work to better your business, request a demo today.