Best Accounting Software for Nonprofits (2026)

Aplos is the only tool in this comparison built from the ground up for nonprofits and churches, and it shows. Funds are a core part of the chart of accounts rather than a tag bolted on afterwards, so restricted grants and designated gifts are separated from the moment a transaction is entered. Every plan includes a balance sheet and income statement by fund, a board portal and 1099 management.

The other big advantage is that donations and accounting live in one system. Online gifts flow straight into the books, and year-end giving statements take a click instead of a mail merge. For a small team, that removes a whole reconciliation step.

Which plan to pick: Lite covers basic fund accounting and reporting. Most growing organizations will want Core, which adds accounts payable and receivable, basic budgeting, recurring transactions, period close and user permissions. Aplos recommends Advanced for organizations with more than $250,000 in annual revenue; it adds budgeting by fund, grant, department or project and dimensional reporting.

Watch out for: the user limits. If more than two staff members need access, you will be on Advanced or a custom plan sooner than the revenue guideline suggests.

QuickBooks Online is not nonprofit software, but it is the default choice for a reason: your accountant almost certainly knows it, and there is an app for nearly everything. Nonprofits typically use classes to stand in for funds or programs and locations for sites or chapters, then run reports filtered by class.

That approach works well when your restricted funds are few and simple. It gets fragile as grants multiply, because nothing stops a transaction from being posted without a class, and there is no built-in balance sheet by fund.

Which plan to pick: skip Simple Start ($38/mo) and Essentials ($74/mo); neither includes class tracking. Plus at $115 per month is the realistic starting point for a nonprofit, with 5 users, up to 40 classes and budgeting. Advanced at $275 per month adds unlimited classes, 25 users and custom permissions.

Watch out for: donations. QuickBooks has no donor database, so you will need a donor management tool that syncs to it.

Xero’s biggest draw for nonprofits is that it never charges per user. Board treasurers, program managers and an outside bookkeeper can all have logins without the bill going up, which is rare at this price.

Like QuickBooks, Xero has no native fund accounting. Nonprofits use tracking categories to tag income and expenses by fund or program and then filter reports. That is workable for a handful of funds but needs discipline.

Which plan to pick: Early at $25 per month is fine for a very small organization, but its limit of 20 invoices and 5 bills per month is easy to hit. Growing at $55 per month removes those limits and adds budgeting (3 budgets). Established at $90 per month adds multi-currency, project tracking and expense claims.

Watch out for: the price change. Xero states that subscription prices increase from October 1, 2026, so check the current price before you commit.

Sage Intacct is where nonprofits often land when they outgrow QuickBooks: many grants with different reporting periods, several programs or entities, and auditors who want clean, consistent reports. Its dimension-based design lets you slice the same transaction by fund, program, grant, department and location without maintaining separate charts of accounts.

The trade-off is cost and complexity. Sage builds each quote from the modules you need, and implementation is typically done with a partner. For an organization with a small staff, Aplos or QuickBooks Online will be faster to run and cheaper to own.