How Ecommerce Payment Reconciliation Works
TL;DR:
- Reconciliation confirms your sales match your payments, fees, and refunds.
- High transaction volumes and multiple payment providers make manual checks unreliable.
- Automated reconciliation imports data from all platforms (Shopify, Magento, PSPs, banks) and matches it in minutes.
- Regular reconciliation protects cash flow, prevents write-offs, and speeds up month-end close.
- Use automation to track exceptions, maintain searchable audit trails, and assign ownership.
- Monitor key metrics: auto-match rate, exception resolution time, and unreconciled value.
- AI and real-time reconciliation are the next frontier, especially for crypto and instant payments.
- Firms like Buster + Punch cut reconciliation time by over 90% with automated processes by working with Aurum Solutions.
- Automation is no longer optional. It’s the only scalable way to keep ecommerce finances accurate and compliant.
What Is Ecommerce Reconciliation?
Defining Ecommerce Payment Reconciliation
Ecommerce payment reconciliation is the process of verifying that the payments recorded in your sales channels match the actual funds received in your accounts. In other words, it’s checking that every customer order corresponds to a completed payment, and accounting for any differences. This includes matching up sales with bank deposits and factoring in things like refunds, chargebacks, fees, and loyalty rewards. The aim is to ensure your financial records across platforms (ecommerce site, payment gateways, bank statements) are consistent and correct.
A comprehensive ecommerce reconciliation doesn’t stop at payments. Leading online retailers also reconcile inventory movements (to confirm stock sold matches stock shipped or returned), commissions (e.g. affiliate or marketplace fees), and taxes (ensuring VAT/sales tax collected aligns with what’s reported). In short, it’s about making sure every piece of the financial puzzle – cash, stock, fees, and more – aligns across systems.
Difference from Traditional Retail Reconciliation
Traditional brick-and-mortar reconciliation typically deals with one point-of-sale system and a daily bank deposit, making it relatively straightforward. Ecommerce reconciliation is more complex. Online businesses deal with multiple payment methods (credit cards, digital wallets, buy-now-pay-later services), many sales channels (website, marketplaces, social stores), and often international transactions in different currencies. Transactions happen 24/7 and might settle at different times. This high volume and diversity means manual processes (like tallying receipts) are impractical for ecommerce.
“The beauty of ecommerce isn’t just that merchants can sell to more people, they can also have more people selling for them in the form of affiliates. However, this system comes with additional complexity - affiliates receive different rates, their rates change if they sell ‘add-ons’ or ‘bundles’, and more. Ultimately, various factors can impact what affiliates are paid, meaning it’s crucial that there’s a central point which can ingest and reconcile data on rates, sales, and payments completion, ensuring that they receive what they’ve earned.”
Robert Mattila-Gilbert, Delivery Solution Architect at Aurum Solutions
The Evolving Landscape of Ecommerce Finance
The ecommerce landscape is constantly shifting. Omnichannel retail (blending online and in-store sales) has introduced new reconciliation challenges as orders and returns cross channels. Payment innovation is rapid – from mobile wallets to cryptocurrency – and each new method adds reconciliation overhead. Transaction volumes keep climbing, and faster payment processing (even instant payments) means back-office processes must keep up in near real time. Furthermore, cybersecurity risks and system outages have shown that businesses need resilient, automated reconciliation to recover quickly . The bottom line: ecommerce firms face growing complexity, and staying on top of reconciliation requires more sophisticated tools and processes than ever.
Key Stakeholders in the Reconciliation Process
Accurate reconciliation benefits many roles in an ecommerce business:
- Finance & Accounting: Own the process, ensuring the books are accurate and compliant.
- Ecommerce Managers: Need reconciled payment data to confirm every order was paid and to analyse sales performance without missing revenue.
- Operations/Warehouse: Rely on reconciled order and inventory data to ensure only paid orders ship and stock levels are correct.
- Payments/Fraud Teams: Use reconciliation to spot missing payments, resolve chargebacks faster, and flag suspicious discrepancies.
- Executives & Auditors: Gain confidence that all transactions are accounted for. Robust reconciliation builds trust with leadership and regulators by proving financial accuracy.
Scorecard: Do you need to automate your ecommerce reconciliation?
Tick every box that is already true in your business.
❏ Do you process more than 1,000 ecommerce transactions a month?
❏ Do you sell through multiple channels (B&M, Shopify, Marketplaces, Retailers, etc.)?
❏ Do you work with more than one payment service provider (Stripe, PayPal, Klarna, etc.)?
❏ Do you handle more than one currency or operate internationally?
❏ Does your reconciliation process take more than one business day?
❏ Do unresolved discrepancies or aged items carry over each month?
❏ Is your reconciliation done mainly with spreadsheets or manual uploads?
❏ Do you lack real-time visibility into exceptions or missing payments?
❏ Do you spend more time investigating transactions than analysing results?
❏ Are you expanding into new markets, currencies, or payment types (BNPL, crypto)?
Your result:
0–3 🟢 Manual reconciliation still manageable, but monitor efficiency.
4–5 🟡 You’re losing time and visibility. Automation will save hours and protect cash flow.
6+ 🔴 Automation is urgent. Manual reconciliation is already a compliance and revenue risk.
Key Stages in the Ecommerce Reconciliation Process
The reconciliation process typically follows these stages:
1. Data Collection and Aggregation
Gather all transaction data from every source:
- Sales Orders: Export orders from all your sales platforms (e.g. Shopify, Magento, Amazon) with order IDs, dates, amounts, etc.
- Payment Provider Reports: Collect reports from gateways/processors (Stripe, PayPal, Klarna, etc.) showing payments received, fees, and payouts.
- Bank Statements: Pull bank records showing deposits from those providers (and any direct payments).
- Other Records: Include data on refunds, chargebacks, discounts, and any loyalty or gift card usage.
Consolidating this data is crucial. Automation helps by importing data via APIs (Aurum offers hundreds of integrations ) so nothing is missed. You want all internal and external records in one place for easy comparison.
2. Transaction Matching and Verification
Match each order against the corresponding payment and verify details:
- Orders to Payments: Ensure every order has a matching payment in your gateway or bank records (check amounts, dates, IDs). Any order without a payment (or vice versa) is an exception to investigate.
- Amounts & Fees: Verify the numbers line up after accounting for fees and currency exchange. For example, if a £100 sale results in a £97 deposit (after £3 in fees), your records should reflect that net amount.
- Partial or Batch Payments: Handle scenarios like instalment payments or aggregated marketplace payouts. Make sure all parts of a split payment or all orders in a batch deposit add up correctly and are received.
- Taxes and Adjustments: Confirm that any sales tax or VAT recorded matches what was actually received (or will be remitted), and that discounts or coupons are properly reflected in final paid amounts.
This step confirms you got the right funds for each sale. Modern reconciliation tools can auto-match the majority of transactions using smart rules, drastically reducing manual work. (One Aurum client auto-matched over 99% of transactions .) By the end of matching, you’ll have a short list of any unmatched or mismatched items to resolve.
3. Updating Loyalty Program Totals
If you offer loyalty points or store credit, include them in reconciliation. Ensure points are only awarded for successful, paid transactions, and subtract points for any refunded or cancelled orders. Make sure the loyalty ledger matches reality – no customer should keep points for a purchase they didn’t pay for. Reconciling these balances protects you from liabilities drifting upward due to unearned rewards.
4. Discrepancy Resolution and Investigation
Investigate and resolve any exceptions identified:
- Flag & Investigate: For each unmatched transaction or amount discrepancy, determine the cause. It might be a timing delay (payment arriving a day late), a data error, or a missing fee. Check supporting details and reach out to payment providers if needed.
- Resolve or Escalate: Correct records or post adjusting entries as appropriate. If a payout is missing, contact the provider. If an order was never actually paid, adjust your revenue and follow up as needed. Have an escalation plan for any large or ageing issues (e.g., alert management if an unreconciled amount exceeds a threshold or age).
- Track Outstanding Items: Maintain a dashboard or log of open discrepancies and how long they’ve been unresolved. This ensures nothing slips through the cracks. High visibility into aged unreconciled items (via reports or alerts) lets you prioritise and close them out.
Every resolved discrepancy brings your books back in balance. Keeping a documented audit trail of these fixes is important for compliance and audit purposes.
5. Financial Integration and Reporting
Integrate the results back into your finance systems and produce reports:
- Sync to Accounting: Post journal entries to reflect the reconciled totals. For example, automatically record payment fees, update revenue for actual settled amounts, and clear any temporary holding accounts. Aurum’s software can perform bidirectional journal sync, pushing entries into your ERP so your ledger matches the reconciled reality.
- Generate Reports: Create reconciliation reports showing total orders vs. payments received, any unresolved exceptions, and adjustments made. You might also prepare specific reports like affiliate commission statements (using reconciled data to pay partners accurately) or daily cash position updates for management.
- Audit & Compliance: Retain all reconciliation documentation and logs. If regulators or auditors need proof of reconciliation (e.g., for FCA client money rules or tax audits), you can readily provide it. A well-audited reconciliation process demonstrates fiscal responsibility and instils confidence.
By the end of this stage, your internal records, bank accounts, and platform data should all align. Management can trust the financial data, and stakeholders can be assured that no money has fallen through the cracks.
Optimising Ecommerce Reconciliation Through Technology and Best Practices
To master reconciliation, combine powerful software with smart processes:
Automation Solutions for Reconciliation Challenges
Manual reconciliation is too slow and error-prone for modern ecommerce. Automation is the key to staying efficient and accurate. Reconciliation software automatically imports data from your systems, performs high-speed matching, and applies rules for common issues. It can also schedule tasks (e.g. run every night) so each morning you start with the previous day’s transactions already reconciled. Plus, automation provides full audit trails, reducing human error.
“Whilst an international presence can make the overall operations of an ecommerce company more resilient to the performance of individual markets, it does add complexity to their financial back office. This is especially true in the current climate of taxes and tariffs regularly changing. When working towards accurate financial numbers, FinOps teams therefore need to be mindful not only of the differing taxes across the world but also how nations apply them to different types of products.”
Tim Andrews, Chief Solutions Architect at Aurum Solutions
Companies that embrace these tools often see dramatic improvements (reports of reconciliation time and errors dropping by 80–90% are common). You can read Buster & Punch's success story here.
When choosing a reconciliation solution, look for:
- Integration: It should connect easily with your shopping platforms (Shopify, Magento, etc.), payment providers, banks, and accounting software. Quick integration means you can onboard new channels or PSPs fast and keep everything in sync.
- Flexibility: The tool must handle your data formats and business rules. Ensure it supports multiple currencies and custom matching logic unique to your needs.
- Scalability & Security: As you grow, the software should handle increasing volumes without slowing down. And since it deals with sensitive financial data, robust security (encryption, permissions, audit logs) is a must.
Best Practices for Efficient Reconciliation
Even with great software, following best practices maximises your efficiency:
- Reconcile Frequently: Don’t wait until month-end. Daily or weekly reconciliation prevents backlogs and catches issues when they’re easier to fix.
- Standardise & Include Everything: Use consistent IDs and formats across systems to make matching easier, and account for all fees, commissions, and taxes so nothing is overlooked.
- Address Exceptions Promptly: Keep a close eye on your exception list. Investigate and resolve discrepancies as soon as they arise. Quick action can recover missing funds (like a payout that didn’t arrive) before it impacts your business.
- Document and Improve: Maintain documentation for your process and note recurring issues. If you see patterns (e.g. a particular gateway often has missing transactions), fix the root cause or adjust your rules. Continuously refine your process, so each cycle gets smoother.
For example, by reconciling daily and automating most steps, retailer Buster + Punch achieved a >90% reduction in reconciliation time and now easily handles thousands of transactions per day. They also gained clear visibility into outstanding issues, enabling their team to resolve exceptions faster. Adopting a similar approach – frequent cycles, automation, and diligent follow-up – will ensure your ecommerce operations remain financially accurate and scalable.
“Ecommerce firms face many reasons why their data might not reconcile. Paired with a high volume of transactions, this risks their aged items report of unreconciled items growing to the point that they could be forced to write off losses. Their exception management therefore deserves to be equally well-developed as their reconciliation; searchable audit trails and automatic exception categorisation and assignment are just some tools to make this process easier.”
Clément Bourcart, Head of Solutions at Aurum Solutions
Measuring Reconciliation Performance
It’s wise to track a few KPIs to gauge your reconciliation process:
- Auto-Match Rate: The percentage of transactions matched automatically (the higher, the better – many strive for 95%+).
- Exception Resolution Time: How quickly you clear discrepancies on average.
- Unreconciled Amount: The total value of transactions not yet reconciled (ideally near zero at period-end).
Improvements in these metrics signal a healthier process. Organisations that adopt automation often see these numbers improve significantly – auto-match rates can exceed 98%, and what once took days now takes minutes. Use these measurements to identify bottlenecks and see your process become more efficient.
Future Trends in Ecommerce Reconciliation
Looking ahead, several trends will shape ecommerce reconciliation:
- AI & Machine Learning: Artificial intelligence will increasingly help predict matches and detect anomalies automatically, further reducing manual work.
- Real-Time Processes: With faster payments and higher customer expectations, reconciliation is moving toward a continuous, real-time process. This gives you an up-to-the-minute view of cash flow as transactions stream in.
- Crypto & New Payments: As more businesses accept cryptocurrencies and alternative payment methods, reconciliation tools are evolving to integrate blockchain transactions and crypto-to-fiat conversions. Expect solutions that seamlessly reconcile crypto payments alongside traditional ones.
Staying ahead of these trends will help you future-proof your reconciliation strategy. By investing in smarter automation and keeping your processes agile, you can ensure financial accuracy and trust even as ecommerce finance evolves rapidly.
Book a personalised demo today and ensure you stay ahead of the trends, with a future-proof reconciliation process and software.
Fiscal Responsibility Statement
At Aurum Solutions, we are committed to upholding fiscal responsibility in all our financial endeavours. We prioritise prudent financial management, transparency, and accountability to ensure the effective allocation and utilisation of resources. Our commitment to fiscal responsibility extends to our stakeholders, fostering trust and sustainability in our financial practices.