How Automation Solved 90% of Payment Reconciliation Problems
September 10, 2025 · 10 min read
Running an e-commerce business sounds exciting, until you're manually reconciling payments across marketplaces like Amazon and Myntra. Each platform comes with different rules, file formats, payout dates, and deductions. One of our clients, a growing e-commerce seller, used Zoho Books for bookkeeping but spent hours weekly downloading Excel files and uploading them manually. It was exhausting and slowing down growth.
That’s where Complere Infosystem stepped in. We automated the entire process, enabling real-time data syncing between marketplaces and Zoho Books. So, as a result 90% of reconciliation was handled automatically.
Why Automation Matters for E-Commerce Businesses
Today in almost every multi-channel e-commerce world, sellers often operate across platforms like Amazon, Flipkart, Myntra, Shopify, and more. Each of these platforms has its own formats, policies, and payout cycles. Trying to manage all this manually can quickly become overwhelming and costly. If you're an e-commerce seller dealing with more than one platform, automation is essential for survival and growth.
You risk human errors: Manual reconciliation often involves copying and pasting data from different Excel files. A small mistake can throw off your entire balance sheet, misreport income, or result in missed payments or refunds.
You lose hours of productivity: Every hour spent manually reconciling transactions is an hour not spent on marketing, product research, or customer experience things that actually grow your business.
You delay decisions based on incomplete data: Without real-time data syncing, you’re always looking at yesterday’s data. This affects your ability to make quick pricing changes, restock inventory, or respond to sales trends.
You increase compliance and audit risks: Mistakes in reconciliation can lead to errors in tax filing, inaccurate financial statements, or problems during audits. Automation ensures a consistent and traceable data trail.
With payment automation systems in place, reconciliation becomes a seamless background process. You no longer need to worry about missed reports or misaligned payouts. Platforms like Zoho Books automation are designed to work hand-in-hand with API integration and automation tools. This offers reliable syncing, timely notifications, and clear financial visibility.
The Secret to 90% Less Manual Work in E-Commerce Reconciliation
Tired of downloading reports, fixing mismatches, and manually uploading data into Zoho Books? You’re not alone. In this short video, Isha Taneja shares how one e-commerce seller fixed it all with a smart automation strategy.
Whether you're selling on Amazon, Myntra, or any other platform—this real-world solution shows how automation can save time, cut errors, and simplify your entire reconciliation process.
How Automating Payment Settlements Is Effective for Multi Platform Sellers | Isha Taneja | Complere
The Problem: “Manual Payment Reconciliation Chaos”
E-commerce sellers juggle a lot—inventory, orders, returns, and customer service. But one of the most time-consuming parts is payment reconciliation. It's the process of matching platform payouts with order details, returns, fees, and taxes.
Our client’s issue wasn’t unique. Like many sellers, they relied on Excel spreadsheets for managing financial entries across platforms. Each platform gave different reports in different formats, and reconciling these with Zoho Books involved:
Downloading sales and payout files
Manually matching transactions
Uploading data into Zoho Books
Identifying mismatches and errors
This repetitive work was draining valuable time and resources. Even worse, the errors and delays in reconciliation led to missing refunds, overlooked payouts, and inaccurate profit tracking.
The Solution: “Smart Automation Approach with API and RPA”
We knew this wasn’t just a bookkeeping issue, it was a data integration problem and data automation. The solution? Eliminate manual steps with automation.
How we solved it step-by-step:
Step 1: API Integration
For platforms like Amazon that provide APIs, we created direct connections to fetch payout, commission, and transaction data in real time. These API integrations pulled data on a daily basis and synced it directly into Zoho Books automation without any human effort needed.
Step 2: RPA for Non-API Platforms
Some platforms didn’t have public APIs or made integration complex. For these, we deployed Robotic Process Automation (RPA). Our bots logged in, downloaded the required reports, cleaned the data, and uploaded it to Zoho Books just like a human—but faster and without errors.
Step 3: Centralized, Real-Time Sync
Whether through API integration or RPA, all data now flowed into a central system. Real-time data syncing kept financial data accurate, timely, and accessible—anytime the client needed it.
The Results: 90% of Reconciliation Automated
The impact of automation wasn’t just noticeable—it was transformative. What used to be a frustrating, manual task became a smooth and reliable process. The improvements were both immediate and measurable, giving the business a significant operational boost.
1. 90% of payment reconciliation was fully automated
The majority of transactions from Amazon, Myntra, and other marketplaces were matched and recorded without any human intervention.
2. Zero manual downloads or uploads
The days of juggling Excel sheets were gone. More accurate reports with real-time data syncing. Everything was fetched, cleaned, and processed automatically.
3. More accurate reports with real-time updates
With data flowing in directly from APIs and RPA bots, there were fewer errors, no missing entries, and reports that reflected the current state of the business—not last week’s.
4. Faster month-end closings
The finance team no longer had to scramble to reconcile books at the end of each month. The books were always up-to-date, reducing close time from days to hours.
5. Reduced dependency on manual labor
Instead of hiring additional staff or spending internal resources on repetitive tasks, the business could rely on automation to handle scale with ease.
More Opportunities with Automation
This solution doesn’t just apply to reconciliation. So, if reconciliation is your first pain point, it’s also your starting point for broader operational transformation. Once the foundation is in place, automation tools can transform other core operations:
Inventory syncing across platforms
Order-to-cash tracking
Automated tax calculations
Return and refund validations
Sales channel analytics in real time
Final Verdict
Manual reconciliation issues are outdated in the digital-first world. As marketplaces grow, sellers must adopt smarter tools to stay ahead. Whether you’re dealing with two platforms or ten, automation powered by API integration and Robotic Process Automation (RPA). This can take the burden off your team and bring clarity to your books. We helped one seller automate 90% of their reconciliation efforts. If you’re spending more time managing reports than running your business, now is the time to explore payment integration and automation for your operations.
Tired of wasting time on manual reconciliation? Click here to adapt automation and simplify your business
Payment reconciliation ensures that the money deposited in your account matches your sales, fees, and returns across platforms—keeping your financial records clean and accurate.
APIs create real-time connections between marketplaces (like Amazon or Flipkart) and tools like Zoho Books, removing the need for manual uploads.
You can use Robotic Process Automation (RPA) to simulate human activity—automating downloads, logins, and uploads to Zoho Books.
Not at all. Even small and mid-sized sellers benefit. Automation improves accuracy, saves time, and allows teams to focus on growth instead of admin work.
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Complere Infosystem is a multinational technology support company that serves as the trusted technology partner for our clients. We are working with some of the most advanced and independent tech companies in the world.
