Ecommerce payment reconciliation software is one of the easiest ways to clean up your books without drowning in spreadsheets. These tools automatically match your orders, payouts, fees, taxes, and bank deposits, giving you accurate books and a clearer picture of your cash flow.
If you sell on Shopify, WooCommerce, or across multiple channels, you already know how messy payment gateways can get. Missing payouts, mismatched deposits, and unexplained fees add up fast. Reconciliation software fixes that by automating the entire process and flagging issues before they become costly.
But with so many tools built for different business models, choosing the right one isn’t always straightforward. This guide breaks down the top 5 ecommerce payment reconciliation tools so you can quickly find the best fit for your store, your workflows, and your budget.
Top 5 Ecommerce Payment Reconciliation Software Compared
Before we dive into our comparison, here’s a quick look at what each solution brings to the table:
| Name | Best for | Starter price | Key features |
| MyWorks | Small to mid-sized ecommerce businesses | $20 per month | Automatic sync
Custom mapping Support for inventory Multi-store support Deep integration |
| Ledge | Venture-backed startups and fast-scaling tech businesses with high transaction volumes | Upon request | Real-time reconciliation
Data analytics Multi-channel support |
| Stripe | Online companies selling across multiple international markets | 2.9% + $0.27 per successful transaction | Automated deposit matching
Fee and chargeback tracking Custom financial reports |
| Taxilla | Large enterprises and multinational corporations in high-risk sectors | Custom | Compliance support
ERP and accounting integration Multi-payment processors |
| Eshopbox | Medium to large-sized commerce brands selling predominantly through online marketplaces | Custom | Instant alerts
Financial reporting Claims and recovery support |
MyWorks
MyWorks is an ecommerce accounting sync that streamlines manual data entry by automatically syncing transactions between your website and accounting software. It keeps sales, fees, and refund data flowing smoothly between ecommerce and accounting, so your books are always up to date. That means when you go to QuickBooks and Xero, you don’t have to manually enter sales data because everything is already in its right place.
Key Features
- Automatic sync: MyWorks lets you choose how often you sync your books, with the option to sync data in real-time.
- Custom mapping: you can map categories from your online store to your books to create your preferred setup.
- Support for inventory: in addition to sales and orders, MyWorks tracks inventory to help you avoid overstocking or stockouts.
- Multi-store support: MyWorks can sync data from multiple stores into a single account, keeping your books organized no matter the size and complexity of your business.
- Deep integration: you can manage your QuickBooks or Xero store from within your store dashboard, making bookkeeping faster to manage.
Best For:
Small and mid-sized ecommerce businesses that want automated reconciliation without managing spreadsheets or juggling multiple dashboards. Especially ideal if you rely on QuickBooks Online, QuickBooks Desktop, or Xero.
Ledge
Ledge automatically matches ecommerce transactions across multiple sources, including your store and payment gateways. You can decide whether to reconcile between two or more platforms based on your needs.
If something doesn’t add up, like there’s a missing payment or unexpected fee, Ledge flags the issue for you to review.
Key Features
- Real-time reconciliation: Ledge matches transactions from your website and payment processors as they happen.
- Data analytics: you can consolidate data from across your gateways and channels into one unified view on the dashboard.
- Multi-channel support: Ledge gives you the option to reconcile one-to-one, one-to-two, or one-to-many.
Best For:
Tech-forward, high-volume businesses selling through multiple payment gateways and marketplaces that need instant visibility into transaction gaps or errors.
Stripe
You’re probably familiar with Stripe as a payment processor. But did you know it also helps businesses stay organized with its native reconciliation features?
When a customer makes a purchase from your store, Stripe automatically matches the purchase with your bank deposit. It keeps tabs on fees, refunds, and chargebacks along the way to ensure complete accuracy.
Key Features
- Automated deposit matching: Stripe compares records like invoices and fees with bank statements to check they match.
- Fee and chargeback tracking: You can break down processing fees and refunds so it’s simpler to monitor deductions.
- Custom financial reports: Stripe gives you visibility into every stage of the transaction to give you more insights into your cash flow.
Best For:
DTC or SaaS-style brands using Stripe as their primary payment processor and wanting native reconciliation without adding new software.
Taxilla
Taxilla reconciles sales, payment receipts, and returns by matching transactions across accounting and enterprise resource planning (ERP) software. It pulls data from multiple sources to check your records match and notify you about any discrepancies. Beyond matching numbers, Taxilla also helps you track how payment adjustments affect cash flow to give you a clearer idea of where money is going.
Key Features
- Compliance support: Taxilla has controls to ensure you don’t overage on any marketplaces and handle disputes properly.
- ERP and accounting integration: You can connect with a variety of popular financial systems like Sage and Abacus to maintain consistent records.
- Multi-payment processors: Taxilla can reconcile a high volume of transactions from payment processors across different countries, including APAC, Europe, and Africa.
Best For:
Enterprises that need multi-country compliance tracking, ERP-level reconciliation, and high-volume transaction oversight.
Eshopbox
Marketplace sellers know that tracking payments, fees, and deductions everywhere you sell gets complicated fast. India-based Eshopbox makes it easier by monitoring orders and payments from websites like Amazon and eBay, ensuring you receive what you’re owed. When it notices a discrepancy, it notifies you and explains the issue.
Key Features
- Instant alerts: There will soon be a new feature that alerts you whenever you’re overcharged or a hidden fee is applied.
- Financial reporting: Eshopbox combines all your transaction data into a single report you can access via the dashboard.
- Claims and recovery support: You can easily identify transactions from returns that have not been properly recorded as refunds.
Best For:
Medium to large ecommerce brands (especially in Asia) that sell heavily on marketplaces and need visibility into fee discrepancies, lost payments, and return-related mismatches.
Why You Need Ecommerce Payment Reconciliation Software
As your operations expand across multiple channels and gateways, daily reconciliation becomes increasingly complex. Small discrepancies like missing deposits, incorrect fees, and mismatched payouts quickly compound into lost revenue. Manual checking isn’t scalable. It’s slow, error-prone, and doesn’t offer the audit trail modern ecommerce businesses need.
Ecommerce payment reconciliation software automates:
- Matching ecommerce payouts with bank deposits.
- Flagging missing, duplicate, or mismatched transactions.
- Handling multi-gateway fees and chargebacks.
- Reconciling multiple channels (Shopify, WooCommerce, Amazon, etc.).
- Syncing revenue and fees into QuickBooks or Xero.
- Most tools start around $20 per month, delivering immediate ROI by saving hours of manual bookkeeping each week.
What Features Should You Look For in Ecommerce Reconciliation Software?
Use this checklist when comparing tools:
- Automated reconciliation workflows.
- Customizable mapping (accounts, fees, taxes, products).
- Deep ecommerce integrations.
- Multi-channel and multi-gateway support.
- Scalability (transaction limits, pricing tiers).
- Reliable customer support (ideally 24/7).
Keeping Books Up to Date Without the Chaos
The best ecommerce payment reconciliation software depends on your business model. What works for a marketplace seller may not suit a DTC Shopify store. But the essentials don’t change: choose a tool that simplifies reconciliation, scales with your growth, and removes manual steps; it doesn’t add more.
| Sync Shopify payment data in the way that works for you
MyWorks lets you automatically sync sales, taxes, products, fees, and more from Shopify or WooCommerce into QuickBooks or Xero. |
FAQs About Ecommerce Payment Reconciliation Software
1. Which Tools Offer Automated Reconciliation Between Ecommerce Transactions and Bank Deposits?
Several reconciliation tools offer this feature, but MyWorks provides the most comprehensive automation for Shopify and WooCommerce sellers by syncing payouts, fees, taxes, and deposits directly into QuickBooks or Xero, eliminating the need for manual matching.
2. Are There Tools That Match Ecommerce Payouts and Bank Deposits Automatically?
Yes, MyWorks automatically matches payouts from Shopify or WooCommerce with bank deposits in your accounting software, ensuring every order, fee, tax, and refund is accounted for accurately.
3. What Platforms Help Automate the Process of Reconciling Ecommerce Deposits and Payouts?
MyWorks automates ecommerce deposits and payouts by syncing detailed transaction data into QuickBooks or Xero. This removes the manual work of matching fees, refunds, and settlement amounts to your bank records.
4. Can Any Ecommerce Bookkeeping Software Match Bank Deposits With Marketplace Payouts Automatically?
Yes, MyWorks can automatically match payouts and deposits for Shopify and WooCommerce sellers. Marketplace-heavy sellers may use other tools, but for cart-based stores, MyWorks provides the most accurate and automated reconciliation.
5. Which Solutions Allow for Automatic Reconciliation of Ecommerce Payouts in QuickBooks Online?
MyWorks is the strongest option for automatic Shopify/WooCommerce payout reconciliation in QuickBooks Online. It posts every payout, fee, tax, and adjustment into QuickBooks Online so deposits reconcile accurately without spreadsheets or manual work. Try MyWorks for free.
