How To Handle Online Sales with E-Commerce Reconciliation?


Have you ever wondered why some online businesses thrive while others struggle to keep up with their sales and finances? The answer often lies in how they manage their e-commerce reconciliation. 

For direct-to-consumer brands, restaurant chains, and financial intermediaries, mastering e-commerce reconciliation is necessary. It helps identify discrepancies early, prevent revenue loss, and make informed financial decisions.

Keep reading to explore the essentials of handling online sales through effective reconciliation, and how it can transform your business operations.

What is E-commerce Reconciliation?

The rise of e-commerce has revolutionized the way customers shop. They can now easily purchase products from a company's website or through various marketplaces like Flipkart and Amazon. This accessibility to omnichannel retailing systems offers unmatched convenience for shoppers but presents a significant challenge for finance teams. 

Consider manually sifting through thousands of transactions spread across different sales channels, each involving a variety of payment methods. Add to this the complexity of modern services like buy now, pay later options, dealing with multiple currencies, handling shipping fees, managing product returns, buybacks, third-party logistics fees, and calculating margins. 

The task becomes even more challenging. E-commerce reconciliation is the process of systematically matching every online sale and transaction with bank records to ensure financial accuracy. 

For businesses aiming to streamline this process, e-commerce payment reconciliation software has become an indispensable tool. It automates the tedious task of reconciling transactions across multiple platforms, thereby saving time and reducing errors.

What Challenges Do Businesses Face in E-commerce Reconciliation? 

The process of e-commerce reconciliation is fraught with challenges that can lead to significant profit losses if not appropriately addressed. Here are some of the critical hurdles businesses encounter:


Platforms like Amazon and Flipkart take a cut from the sales as a commission for marketing and selling products. This commission varies and must be accurately recorded to ensure correct profit calculations. The need for a solution like Flipkart payment reconciliation software becomes apparent here, which automatically tracks these deductions and reconciles them with sales.

Payment/Closing Fee

Marketplaces impose additional charges, such as a 'closing fee' on each product sold. This fee can vary, adding another layer of complexity to the reconciliation process.

Shipping Charges

Most marketplaces now offer shipping services, deducting the shipping charges directly from the seller's payment. Errors in recording product details can lead to being overcharged for shipping, necessitating meticulous attention and reconciliation efforts, often facilitated by e-commerce payment reconciliation software.

Storage/Warehousing Fee

Opting for storage services from the marketplace incurs storage or warehousing fees. Sellers must account for these expenses accurately to ensure they're not eroding their profit margins without realizing it.


Discounts can be a double-edged sword. They can either be offered by the seller or the marketplace, with the marketplace deducting the discount before remitting payment to the seller. Sellers must ensure the discounts deducted match the actual discounts offered, preventing losses.

Statutory Taxes

The marketplace deducts all applicable taxes, including service tax on shipping services, before payment is remitted to the seller. This necessitates a thorough understanding and reconciliation of these deductions to ensure compliance and accurate financial reporting.

For businesses operating on platforms like Myntra, utilizing Myntra payment reconciliation services can be critical. These tools and services are designed to tackle the specific challenges presented by each platform, ensuring sellers can reconcile their accounts accurately. 

Best Practices for Effective Reconciliation

Handling online sales effectively requires a meticulous approach to e-commerce reconciliation. Here’s how businesses can enhance their process, ensuring accuracy and efficiency:

  1. Automate Your Reconciliation Process

Automating the reconciliation process is crucial for handling the sheer volume of transactions in e-commerce. Automation can reduce the time spent on reconciliation by up to 70%. By implementing e-commerce payment reconciliation software, a medium-sized retailer can reduce reconciliation time from 30 to 9 hours per week.

This not only speeds up the process but also minimizes errors. For instance, integrating automation reconciliation tools can reduce the time spent by accountants on manual data entry and verification, making the reconciliation of online payments reconciliations more manageable.

  1. Implement Standardized Procedures

The foundation of effective reconciliation lies in standardizing the steps involved:

  • Data extraction: Collecting data from various sales channels.

  • Compilation: Aggregating the data in a unified format.

  • Recording: Logging transactions in financial records.

  • Matching: Aligning transactions with bank statements.

  • Reconciling: Identifying and resolving discrepancies.

By documenting these procedures and using templates, every team member, whether new or existing, can follow the same process, ensuring consistency and reducing the chance of errors. A periodic review of these procedures is also essential to identify areas for improvement or automation.

  1. Incorporate Internal Controls

Incorporating a series of internal checks within the payment reconciliation process can significantly reduce errors. These controls should be tailored to the business's specific needs and integrated into the standardized process. 

By educating every team member about these controls, businesses can ensure and improve the integrity of their financial statements and mitigate risks. An example of this could be double-checking the calculations of commissions and fees deducted by platforms like Amazon or Flipkart to ensure accuracy.

  1. Implementing "Open to Buy" and Multichannel Loyalty Programs

A key practice for managing your online business effectively is adopting financial strategies like "Open to Buy" for inventory control and implementing multi-channel loyalty programs to boost customer happiness. 

"Open to Buy" is a budgeting method that helps plan inventory purchases, ensuring you spend the right amount at the right time to meet customer demand without overstocking. 

Meanwhile, offering loyalty programs across various sales channels rewards and retains customers by giving them value in return for their loyalty. This dual approach streamlines inventory management and enhances customer engagement across different shopping platforms.

  1. Monitor Key Performance Indicators (KPIs)

Regular analysis of KPIs is essential to assess the efficiency of the reconciliation process. Key indicators include:

  • The average time required to complete the reconciliation process.

  • The quality of reconciliations (accuracy on the first attempt).

  • The number of discrepancies identified in each reconciliation.

Setting benchmarks and continuously striving to meet or exceed them can highlight areas for improvement, ensuring the process becomes more efficient over time.

  1. Focus on Upskilling Your Team

The effectiveness of any process improvement or technological adoption relies on the skill set of the team implementing it. Upskilling programs have been shown to improve team productivity. These initiatives enable team members to utilize automated and integrated solutions effectively. 

Training in the latest e-commerce payment reconciliation software not only enhances their ability to perform their roles efficiently but also ensures they can continuously assess and improve the reconciliation process.

  1. Getting to Know Your Payment Gateway

Payment gateways have different ways of handling transactions, including how long they process them, their fee structures, and how they report transactions. It's vital to know these details for proper reconciliation. When reconciling, remember to consider any processing fees, chargebacks, and other possible deductions. This approach ensures you have a clear picture of your finances.

By adopting these strategies, e-commerce businesses can improve their reconciliation processes, ensuring financial accuracy and freeing managerial time to focus on strategic growth and customer satisfaction.

How Does E-commerce Reconciliation Help in Fraud Detection and Prevention?

E-commerce reconciliation is crucial in identifying and preventing fraud by meticulously comparing transaction records against bank statements. 

For example, if an online store records a sale of INR 2000 but the bank statement shows a deposit of INR 2500 for the same transaction, this discrepancy could indicate fraudulent activity or an error in processing. 

By systematically reviewing such mismatches, businesses can quickly spot and investigate unauthorized transactions, overcharges, or undercharges, safeguarding against financial loss and maintaining the integrity of their operations. 

This level of scrutiny ensures that every transaction is legitimate and accurately recorded, protecting the business and its customers from potential fraud.

Why E-commerce Payment Reconciliation with Reconcify

Remember that the future of e-commerce finance leans heavily on automation and intelligent analysis. With Reconcify, stepping into this future is a possibility and a reality. 

By leveraging the power of Robotic Process Automation (RPA) and Artificial Intelligence (AI), Reconcify offers end-to-end automation of the reconciliation process. This simplifies the once-challenging task of matching transactions across multiple channels and ensures accuracy and speed unmatched by manual processes.

Ready to see how it can transform your reconciliation process? Book a demo with Reconcify today and take the first step toward seamless, automated reconciliation.