The best bank reconciliation software should allow you to easily compare your bank statement with your bookkeeping records for the same time period and provide an accurate method for tracking cash flow. It should also enable you to reconcile bank accounts with or without a bank feed connection for maximum flexibility and show all outstanding…
The best bank reconciliation software should allow you to easily compare your bank statement with your bookkeeping records for the same time period and provide an accurate method for tracking cash flow. It should also enable you to reconcile bank accounts with or without a bank feed connection for maximum flexibility and show all outstanding transactions in the reconciliation report.
That said, here are our top six best bank account reconciliation software:
I evaluated each retail accounting system based on how well it supports real retail workflows, including inventory tracking, sales activity, and day-to-day financial management. I focused on what actually works in practice — how transactions flow, how inventory connects to accounting, and how easy it is to manage operations without extra tools.
General features: I reviewed how each system handles core accounting tasks like general ledger, banking, accounts receivable, accounts payable, sales tax, and financial reporting. I gave more weight to platforms that deliver reliable, complete accounting without requiring workarounds.
Retail-specific features: I examined tools that directly support retail operations, including inventory management, sales tax tracking, and POS integration. I prioritized systems that keep inventory and financial data aligned in real time.
Pricing: I compared monthly costs, user limits, and feature availability across plans. I looked closely at whether key retail features are included in entry-level tiers or locked behind upgrades.
Ease of use: I assessed how quickly a non-accountant can complete common tasks like invoicing, expense tracking, and reporting. I focused on navigation clarity and how much setup is required to get started.
Customer support: I reviewed available support channels, including phone, chat, email, and help documentation, to see how easily users can get assistance when needed.
User reviews: I analyzed average ratings from trusted review platforms to understand how each system performs in real-world use.
I determined and evaluated the best bank account reconciliation software using the scoring rubric below.
Methodology weights
Pricing 10%
Bank Reconciliation Features 40%
User Reviews 20%
Ease of Use 20%
Customer Support 10%
We considered the price in three levels: for one user, three users, and five users. As the number of users increases, we’d want to see a more affordable per-user rate if compared to a single user. Besides that, we also awarded points for free trials, monthly plans, and discounts for new customers.
As the meat of our evaluation, bank reconciliation gets the highest weight in the overall score. The major features that we’re looking for are the ability to import bank transactions through feed, upload bank statements, and reconcile manually. The software should also show the outstanding checks and deposits in transit for tracking outstanding transactions. Besides that, the reconciliation report should show the details about why the book and bank balances differed during the reconciliation period.
We looked at user review websites to gauge actual feedback from users. Our score is derived from the average user review ratings from these review websites.
Our ease of use evaluation focused on the overall user experience in performing bank reconciliations. We subjectively rated the overall look of the reconciliation screen, the layout and presentation of the reconciliation report, and difficulty of using the bank reconciliation module.
We considered customer support for customers who might need technical support in using the software. Customers must have access to different support channels for maximum flexibility. In our scoring, providers with multiple support channels receive more points.
3 Ways Accounting Software Perform Bank Reconciliations
There are three basic ways that accounting software can perform bank reconciliations. I recommend that you decide which method you prefer and then choose a software that allows for it. The three methods form a spectrum of functionality, and I’ve listed them, starting with the simplest but least useful.
1. Matching the Book Balance to the Bank Balance
Many free or inexpensive software don’t actually perform what accountants consider to be a true bank reconciliation. While they label the feature as a reconciliation, they don’t allow for any timing differences—i.e., reconciling items—between the books and the bank.
These software only match the balance per the books to the balance per the bank. The accounts must match perfectly for you to finalize the reconciliation, so if you have a paper check deducted on your books that hasn’t cleared the bank, you won’t be able to finalize your reconciliation. You’ll be forced to delete or change the date of the check on your books—both of which will make your books incorrect.
While excluded from this guide, popular software with this very limited bank reconciliation feature include Wave, FreshBooks, and the free version of ZipBooks.
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2. Manual Bank Reconciliation
Prior to the internet, the vast majority of accounting software allowed you to reconcile the bank account per your books to a paper bank statement. Essentially, you manually enter your bank statement balance and then mark transactions in your books that appear on the bank statement. Once reconciled, a report will show all the transactions that have cleared the bank and all the transactions that are reconciling items between the bank statement and the book balance.
Paper reconciliations are great, and many accountants at small businesses still prefer them because they avoid the need to connect your bank accounts to your accounting software. They’re simple to perform, but if you have hundreds of transactions per month, then you’ll want an automated reconciliation. Software in this guide that allow reconciling to a paper statement include QuickBooks, NCH Express Accounts, Sage 50, and AccountEdge. Xero and ReconArt do not allow manual bank reconciliations.
You can learn more about the general process through our guide on
Advanced software like QuickBooks Online automates most of the reconciliation process. The underlying process is the same as reconciling to a paper statement, but the software imports the bank transactions and then automatically compares them to the book transactions. Most software attempt to automatically match bank transactions to book transactions.
During the reconciliation—instead of matching to a paper statement—you’ll confirm the matches between bank and book transactions that the system made and manually match any remaining transactions. A book transaction is considered to have cleared the bank once it is matched to a bank transaction—the equivalent of placing a mark next to it in a manual reconciliation.
Automated bank reconciliations require either a live bank feed or uploading your monthly bank statements. It can be a bit difficult to learn for non-accountants, but automated reconciliations can save a lot of time when dealing with hundreds or thousands of transactions. All of the software on this list import bank transactions to automate the bank reconciliation, but NCH Express doesn’t offer suggestions for likely matches between bank and book transactions.
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Frequently Asked Questions (FAQs)
Some important features to look for include automatic transaction matching, the ability to import bank statements, user-defined rules for matching transactions, and the ability to generate reports and export data.
Bank account reconciliation software can save your business time and reduce errors by automating the process of reconciling bank statements with internal accounting records. It can also help identify and correct errors more quickly and provide an accurate picture of your company’s financial health.
Bank reconciliation software typically connects to a company’s bank accounts and imports transactions into the software. It then matches these transactions with the company’s internal accounting records, such as invoices and receipts, to identify any discrepancies. It can also typically flag transactions that need further investigation or review.
Bottom Line
We chose QuickBooks Online as the best bank account reconciliation software, while Xero is an excellent scalable solution. If you’re looking for accounting software with automated workflows, Sage 50 Accounting is a good choice, whereas ReconArt is ideal for businesses with many transactions. NCH Express Accounting is sufficient if you don’t need bank connections, and AccountEdge is an affordable option for desktop-based bank reconciliation.
Mark Calatrava is an accounting expert for Fit Small Business. He has covered more than 50 accounting software for small businesses and niche industries and has developed an in-depth knowledge of the important features of accounting software, including how the importance of these features vary by business. As a QuickBooks ProAdvisor, Mark has extensive knowledge of QuickBooks products, allowing him to create valuable content that educates businesses on maximizing the benefits of the software.
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