Nonprofits deal with specific set of financial, accounting, and tax difficulties to gain or maintain their status. Standard accounting software is sometimes prohibitively expensive, and a dedicated bookkeeper may be out of the question.

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Nonprofit accounting software comes in several different forms, and not all solutions meet the needs of every organization:

  • Dedicated nonprofit accounting software provides a solution to this problem, with specialized funding, contact organization, and tax compliance features. These options simplify accounting for many organizations, but they can run on the pricey side.
  • Accounting software with nonprofit-friendly features is another option, but will require some time investment to get up and running.
  • The least expensive but most time-consuming options are free accounting software programs. Think of these as accounting facilitators: you’ll need a dedicated accountant or bookkeeper with significant experience to use these programs successfully, but they’re free.

Browse options for the first two categories below:

Dedicated Nonprofit Accounting Software


Aplos nonprofit accounting dashboard

Nonprofit organizations and churches will find a dedicated nonprofit accounting, fundraising, and donor management system with Aplos. They offer a free, 15-day trial of their direct double-entry software that handles accounting, budgeting, and true-fund accounting. You’ll have complete control over your contributions management with statements and reporting.

Track individual donors through bulk donation uploads and online transactions. Aplos will integrate with 3rd-party donor management apps like Kindful and Bloomerang to keep your donor lists up to date, and you can add donor relation capabilities for a monthly fee. Manage donations on your organization’s website with recurring or one-time debit/credit card transactions.

Aplos even offers support for multiple organizations with roll-up reporting, including outstanding tasks. Free support is available for all subscribers M-F from 8-4. If you want an even better reason to try Aplos, they currently offer a QuickBooks buyback program where they’ll pay $300 to cancel your QuickBooks subscription for Aplos.


FUND E-Z accounting software

FUND E-Z built three separate products with nonprofit needs in mind: fundraising, accounting, and Medicaid. The accounting software includes account charting and different options for your funding source like grants, donations, sites, and departments. Use filters and segmentation to build granular reports and split your transactions across segments.

Secure your data with automatic backups and roll-back protection for all accounts.

Extra features include bank reconciliation, budgeting, and direct/indirect funds allocation. The companion fundraising software includes custom donor fields for your segmented reporting and matching gift functions to organize corporate matching programs. This software will also help you with your fundraising campaigns through email and letter tracking, as well as household or individual donor mailings.

FUND E-Z offers a customized price quote based on your organization’s needs, and there are paid online training classes to help you get setup.

Abila MIP Fund Accounting

Abila mobile accounting interfaces

Abila offers several different accounting systems, including a dedicated non-profit version. Because of its sheer number of features, this software is not for beginners. You’ll want to have an accountant or bookkeeper on-hand to help.

Abila comes hosted in the cloud or on-premise, depending on your security needs. You can track your financials, report internally and externally, and update your systems based on your organization’s changing needs. Print checks and forms from the Abila online catalog. Special features for FASB and GASB compliance come standard.

Of the options listed here, Abila’s system best prepares your organization for tax requirements and audits. It also offers core HR features, association management, and CRM with certain products.

General Accounting Software


Quickbooks accounting dashboard

Intuit QuickBooks is probably the best known accounting software on the market. Although it offers some nonprofit-specific tools, but the program was built mainly for small businesses.

Use the QuickBooks class tracking feature for compliance. Recurring billing sends invoices or receipts to donors automatically. Send your end-of-year donation summary letters with account summaries.

QuickBooks will sync with all your accounts including bank and credit cards, which helps you track all of your accounts in one place. Your online funds transfer apps will also integrate (e.g. Square, PayPal, Method:Donor) and automatically log outside donations that don’t come directly to your bank account.

Sage 50

Sage 50 small business accounting software

Sage offers accounting software for businesses of all sizes, and this is their under-50-users version. While it’s a powerful accounting tool, there’s nothing particularly nonprofit-friendly about it, other than its adjacent CRM and reporting features.

The program itself runs through a desktop client, but you can also access it online for mobile accounting. Features include tab-based navigation, workflow visualizations, reporting, and in-app support documents to help you through setting up the product. Repeat invoicing is available, which is useful for your recurring donations. Build custom income, balance sheets, and cash flow statements.

Sage’s support documents are quite complicated, so this tool is not for the untrained bookkeeper. As with several of the options on this list, you’ll need some accounting background or a consultant to set it up properly.


intacct ERP and accounting

Intacct is a powerful ERP that’s also suitable for nonprofit organizations, especially those that need reporting for multiple organizations under a single plan. This software is unique on this list in that its design is also appropriate for complex philanthropic organizations that supply funding and grants to other organizations.

Intacct’s features include dashboards, reporting, and funds allocation automation built into the system. It also supports project-based accounting that attributes revenue directly to project-specific accounts.


xero mobile accounting options

Xero’s accounting software provides a 25 percent discount for nonprofits and easy uploading of your data from multiple types of legacy systems. Monitor and report on your cashflow, invoicing, payments, and payroll with unlimited users (!) and mobile access.

Invoicing capabilities feature automated recurring payment statements and receipt notifications when they’re opened. You can keep an eye on your financials with custom reporting dashboards and export them to share visibility with other stakeholders.

Xero does address sales and employee tax management, but there is no nonprofit-specific tax information for auditing and compliance purposes.

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Whether you choose dedicated nonprofit accounting software, a general accounting tool, or a free option, you’ll want to take an honest look at your accounting capabilities and the time you’re willing to spend on-boarding. Every accounting tool will require a time investment for implementation, but the surrounding costs and possible bookkeeping fees vary.

Need help building your nonprofit technology stack? Contact our technology advisors. They’ll help you choose the best software options for accounting and beyond.

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