Best bank reconciliation software for nonprofits and churches

Nonprofit bank reconciliation options compared

Every accounting system a nonprofit is likely to run has a reconciliation screen. The differences are in how much of the matching it does for you, how it copes with fund accounting, and what it costs. The table covers the systems US nonprofits use most, plus a dedicated matching tool, with prices as published by the vendor or by TechSoup and Software Advice at the time of writing.

BankReconciler is not an accounting system. It sits beside one: you upload the bank statement and an export of the cash account, and it returns what matched, what is missing from the books and what the bank has not cleared yet. You still record the result in your own ledger.

Which one fits your organization's size

Volunteer-run, under about $250,000 a year. One checking account, maybe a savings account, a treasurer who is not an accountant. The reconciliation is 30 to 80 lines a month, and the built-in wizard in MoneyMinder or QuickBooks Online handles it. Spending more here is hard to justify. What matters more is that someone other than the treasurer reviews it, which we cover below.

Staffed, grant-funded, $500,000 to $10 million. A finance manager or outsourced bookkeeper, payroll, a few restricted grants, online giving and maybe a merchant account. The operating account runs to several hundred lines a month and deposits rarely land as one gift per bank credit. This is where QuickBooks starts to feel thin for fund reporting and organizations move to MIP, Aplos Advanced or Sage Intacct. It is also where reconciliation becomes a day of the close instead of an hour.

Multi-entity or audited every year. A parent organization with a foundation, chapters or a housing affiliate, often a Single Audit. Sage Intacct and Financial Edge NXT are common, with matching rules and bank feeds. Even there, finance teams use a separate matcher for the accounts the feed does not cover, for catch-up after a staff change, or for the month that will not tie.

Why nonprofit bank accounts are harder to reconcile

A business deposit usually equals one invoice. A nonprofit deposit is a stack of gifts, a grant draw and a fundraiser cash box, posted to three funds because restricted money has to be tracked separately. The bank shows one credit. The general ledger shows four lines. Every reconciliation screen that matches one bank line to one book line misses it, and someone ends up adding numbers on a calculator.

Online giving makes it worse. Donation platforms pay out several gifts at once, net of processing fees, a few days after the gift. Unless the fee is posted as its own line, the books never add up to the payout. Grant reimbursements arrive weeks after the expenses they cover, often as ACH credits with a reference number nobody recorded. And volunteer turnover means the person who knows why a $640 check is outstanding from last spring may no longer be around.

If you are on MIP, our page on MIP bank reconciliation walks through these patterns in that module specifically. For QuickBooks, start with bank reconciliation QuickBooks. When the bank only offers a CSV download and QuickBooks wants a Web Connect file, you can convert the CSV bank file to QBO first and import it.

When a dedicated reconciliation tool pays for itself

A separate tool is worth the money in four situations, and not worth it outside them.

• The operating account has hundreds of lines a month. Ticking 400 items in a Reconcile screen takes hours. Matching takes minutes and leaves you the exceptions.
• Deposits are split across funds. BankReconciler tests combinations of up to six ledger lines from the 14 nearest by date for an exact sum, so a deposit posted to three funds matches the one bank credit. The same engine handles matching bank deposits to invoices for businesses.
• The books are months behind. After a bookkeeper leaves or before an audit, reconciling six or twelve months at once with outstanding items carried forward is the fastest route. See catch up bank reconciliation.
• An outside bookkeeper serves several nonprofits. One tool across clients on MoneyMinder, QuickBooks and MIP, each in its own workspace, beats learning four reconciliation screens. That is the case described on bank reconciliation for accountants.

The Starter plan is $49 a month or $288 a year for one organization, three bank accounts and 1,500 transactions a month. Business is $149 a month for five organizations and 15 accounts. You can run one real month before paying. If your monthly reconciliation already takes 20 minutes and ties, keep doing what you do.

The controls auditors look for

Software does not replace segregation of duties, and auditors of small nonprofits flag the same gaps every year. The person who signs checks or records deposits should not be the one who reconciles. The finished reconciliation should be reviewed and signed, with a date, by the treasurer, the finance committee chair or the executive director. Outstanding checks older than six months should be investigated, not carried forever. Reconciling items should be explained in a line, not left as a plug.

A reconciliation report that does not change when someone edits an old transaction is part of that trail. BankReconciler produces a PDF and XLSX bank reconciliation report per account per month with the statement balance, outstanding items and adjusted book balance, which drops straight into the board packet. Lock or close the period in your accounting system too, so late entries cannot move a month that was signed off.

Questions about nonprofit bank reconciliation software

What is the best bank reconciliation software for a small nonprofit?

For a volunteer-run group with one or two accounts, the reconciliation built into a simple cash-based tool is enough: MoneyMinder at $299 a year, or QuickBooks Online donated through TechSoup. Once the operating account has hundreds of lines a month or deposits split across funds, a dedicated matcher such as BankReconciler, from $49 a month, saves the most time.

Can QuickBooks be used for nonprofits?

Yes. Many US nonprofits run QuickBooks Online and track funds and grants with classes or locations, and eligible 501(c)(3) organizations can get a donated subscription through TechSoup for an admin fee. Its Reconcile screen works well for a few dozen items a month. It gets slow on busy accounts and gives no help with deposits split across classes.

How often should a nonprofit reconcile its bank accounts?

Monthly, within a few weeks of the statement date and before the financial report goes to the board. Grant-funded organizations and those facing a Single Audit should treat a monthly reconciliation, reviewed and signed by someone other than the preparer, as the minimum. Very active accounts are often reconciled weekly.

Who should reconcile the bank account in a nonprofit?

Someone who does not sign checks or record deposits. In small organizations that is often a board member other than the treasurer, or an outside bookkeeper, with the treasurer or finance committee reviewing and signing the finished reconciliation. In staffed organizations, the accountant prepares it and the finance director reviews it.

For the wider market beyond nonprofits, including close platforms and AI bookkeeping tools, see the roundup of the best bank reconciliation software.