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Accounting Software for Tax-Exempt Nonprofits

Nonprofits also have to do their accounting. However, since nonprofits have a different accounting structure from for-profits, there are special nonprofit accounting software to help organizations manage their finances such as incoming and outgoing payments, budgeting and reporting.

These programs focus more on the project-focused accounting than on the profits made, and many include tools for accepting donations and presenting figures in a transparent manner to donors and the board.

There are a few things to keep in mind when selecting your software. How easy the system is to learn, the availability of support, how much time it takes to set up – these are all important aspects of selecting software.

If your nonprofit is tax-exempt, then you would also want to look into special 501c3 accounting software to be able to match your requirements

Here are three of the best accounting software for tax-exempt nonprofits.


Aplos is an online option for small to medium-sized nonprofits and religious organizations that is simple and straightforward to use. It allows for easily tracking funds such as grants, customizable donation pages and a Standard plan that includes donations and gift tracking, along with reporting, budgeting, and accounting. The Advanced plan adds to this with fundraising options, and Form 990 reporting as well. Though you will have to pay a little bit to be able to handle your nonprofits tax-exempt reporting, this software is not extremely expensive and allows for a free 15-day trial as well.

Sage Intacct

Sage Intacct has an open API structure that allows you to integrate the accounting system with other business applications where you could be running other aspects of your nonprofit like the payroll or CRM. It has the required features of a general ledger and accounts payable, and allows for purchasing, reporting, and cash management as well.

The Intacct fund accounting helps generate the statement of activities, statement of financial position, cash flows and also the Form 990 that is easily understandable by donors that may want to find out how their investments are coming along. The cost for Sage Intacct depends on the size of the accounting team and the modules that the organization chooses to implement. It also allows the option for a free 30-day trial and an easily accessible demo video.


File990 makes it easier to file nonprofit taxes with a comprehensive software. All you have to do is answer a few simple questions regarding the nature of the organization – no matter how big or small – and File990 does the rest. It is an authorized e-filer with the IRS, and thus submits an organization’s tax returns quickly and securely, making the process as simple as possible.

For larger organizations, File990 also has an enterprise option that provides live updates about individual chapters when they file and sends out reminders as the tax season approaches to make sure you don’t miss any deadlines. Although it is slightly costly, it is a very helpful tool that requires payments per filing session and makes tax filing – which can be quite confusing – a lot easier.

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