The Best Fund Accounting Software

While accountability is essential for every organization, it has an extra layer of importance for charities and non-profits. Luckily, fund accounting software makes it possible for nonprofits, churches, and many other organizations to do their good work. The right accounting solution doesn’t just help maintain financial records, but it also simplifies managing grants, building donor relationships, paying volunteers, and more. To help you zero in on the right alternative for you, we’ve evaluated and ranked the top fund accounting products in the market. Read on!  

The Best Fund Accounting Software

Aplos Logo


Manage Your Finances, People, & Giving For Your Nonprofit Or Church

Designed by a pastor and an accounting professional, Aplos is a popular accounting choice for nonprofits and churches. Used by over 40,000 organizations worldwide, it offers excellent features for fund accounting, donation tracking, membership management, and other critical operational areas.

  • Core features: Double-entry accounting, Invoicing, Payroll, Financial reporting, Donation tracking, CRM, Event management
  • Desktop/Cloud-based: Cloud
  • No. of users: 1 (additional users for a fee)
  • Mobile app: No
  • Customer support: Excellent
  • Base price: $79/month
  • Free trial: Yes
FastFund Logo


FastFund Online handles all your fiscal needs, so you can focus on your mission.

Benefiting from its parent company Araize’s 30+ years of experience providing solutions for the nonprofit sector, FastFund is a feature-packed fund accounting system for nonprofits. Along with robust modules for accounting, fundraising, and payroll, it scores in high-quality training.

  • Core features: Double-entry accounting, Invoicing, Payroll, Financial reporting, Donation tracking, CRM, Event management
  • Desktop/Cloud-based: Cloud
  • No. of users: Up to 5
  • Mobile app: No
  • Customer support: Excellent
  • Base price: $42/month
  • Free trial: Yes
QuickBooks Logo

QuickBooks Enterprise Nonprofit

Accomplish more for your nonprofit

A desktop-based solution designed for nonprofits, this offering from QuickBooks by Intuit can be used to track finances, manage donor lists, and handle payroll tasks. Multiple integrations, online backup of data, and excellent scalability options make it a highly capable solution for fund accounting.

  • Core features: Double-entry accounting, Invoicing, Payroll, Financial reporting, Donation tracking, CRM
  • Desktop/Cloud-based: Desktop
  • No. of users: Up to 40
  • Mobile app: Yes (limited features)
  • Customer support: Excellent
  • Base price: $1,740/year
  • Free trial: No
Oracle NetSuite Logo

Oracle NetSuite

A Responsible, Accessible Approach

A part of Oracle since 2016, California-based NetSuite is known for its cloud business software suite, which includes accounting, ERP, and CRM. Over 30,000 fast-growing businesses worldwide use the product for its comprehensive set of features and high customizability.

  • Core features: Double-entry accounting, ERP, Invoicing, Payroll, Financial reporting, CRM, Ecommerce
  • Desktop/Cloud-based: Cloud
  • No. of users: Undisclosed
  • Mobile app: Yes
  • Customer support: Average
  • Base price: Undisclosed
  • Free trial: No

Selecting the Best Fund Accounting Software

How does one go about picking out the right fund accounting solution from the many options in the market? To shorten the selection process for you, we’ve listed below the key features to look for in fund accounting systems

However, before we get to that stage, it’s vital to understand why we need fund accounting solutions in the first place. Why can’t general accounting software get the job done? Also, what are the expected advantages that should guide our search for the right fund accounting system?

What Is Fund Accounting Software for Nonprofits?

Accounting software for nonprofits, or fund accounting solutions, are designed with the specific needs of nonprofits in mind. The fundamental accounting principles in such software products are the same as in the top accounting software that cater to for-profit organizations. 

That said, there are certain differences in how nonprofit accounting works, meaning, general accounting solutions are not always the best choice. Non-profits and churches often require specially designed accounting solutions to help them in critical areas like bookkeeping, tax compliance, reporting, and grant tracking. High-quality software for churches, government bodies, and nonprofits is also designed to automate many of the related recurring tasks, reducing the time and effort needed to comply with stringent accounting standards.

How Is Fund Accounting Software Different?

The primary difference between accounting products for nonprofits and those for other businesses is in terms of financial standards. Nonprofits rely on grants and donations from different sources to function, which requires them to meet specific standards. For example, nonprofits must file IRS Form 990 every year. Their reporting also needs to meet FAS 116 and FAS 117 standards, which deal with accounting for contributions and accuracy of reporting, respectively.

There are other differences too. Fund accounting software for churches and nonprofits must also help with accounting for donations received in many different forms. This requires specialized tracking and documentation. Plus, the funds have to be deployed in the correct manner, requiring additional software functions to track this aspect.

Another noteworthy difference is that nonprofits often do not have the funds to spare on an expensive product or hire a full-time accounting team. Therefore, it is particularly vital that the fund accounting system handles complex tasks without being costly or difficult to use.

What Are the Benefits of Fund Accounting Software for Nonprofits?

The very reason behind looking for accounting solutions designed for nonprofits is that they bring more benefits than a general accounting solution. It helps to be aware of the advantages you can expect from such solutions, making your search for the right software more goal-focused.

Reduction of manual work

The most significant benefit of a high-quality fund accounting system is the potentially massive savings in time and effort. Most top accounting products today automate tasks like data migration and reconciliation, which are not possible with spreadsheets or simple programs. Many other processes like tracking income and expenses, managing donor relations, and paying staff can be executed more efficiently with the right fund accounting software, leaving you time to focus on core activities.

Data centralization

Nonprofits need to manage different revenue sources and expense categories. If the organization is spread across multiple locations or verticals, consolidating all data for the timely closing of books can be even more stressful. 

Advanced accounting solutions enable faster merging of different databases with the right multi-ledger and multi-entity features. The benefit is not only the elimination of repetitive tasks but also a clearer overview of the organization’s performance.

Streamlined grant management

Nonprofits rely on donations and grants in different forms and from different sources. Some funds have deployment restrictions, while others come with greater spending freedom.

Managing these disparate grant categories is difficult for general accounting solutions. However, the best fund accounting software can tackle this complexity with ease, helping you meet donor requirements and compliance standards.

Better reporting and forecasting

Tracking financial health and managing cash flows is critical for every organization but particularly so for nonprofits that often work with financial constraints. Nonprofit organizations have to manage funds prudently and avoid impact on their initiatives. Top fund accounting systems enable this by helping you make sense of the data in your system. 

You can manage your activities more efficiently and cut down on expenses through the insights provided by fund accounting software for churches and nonprofits. You are also better positioned to approach potential donation sources at the right time and with the right focus.

Greater transparency

Nonprofits are held to higher standards of financial propriety than businesses. This means meeting regulatory standards and providing transparent information to various stakeholders. 

By updating your financial data accurately and on time, advanced fund accounting systems help avoid possible errors that could harm your organization’s reputation. With tools to simplify the filing of required documents, they make compliance stress-free. Finally, with features to create customized reports, they make it much easier to present easy-to-understand information to donors and others.

What Are the Features of Fund Accounting Software?

Your organization will derive the benefits listed above if your fund accounting system has the right features. The features listed below are over and above the general accounting features expected from any high-quality accounting tool and as a result, served as criteria for us while evaluating software solutions. This section can also prove helpful as a general guide in your search for the right accounting software.

Donation tracking

Tracking donations as they move through the system is critical for nonprofits, both to meet regulatory standards and to show donors that their funds are put to good use. The fund accounting software for nonprofits and religious organizations must offer the flexibility to account for different types of donations, including recognizing if the funds have restricted or unrestricted use. 

It is also crucial to track where and how much the funds are used, which also helps with audits. As a result, fund accounting systems often feature tags for funds from different sources or easy identification of tax-deductible income for donors.

Category-wise budgeting

Typically, nonprofits’ expenses fall into different categories. Broadly speaking, one category of expenses is operational, used for utilities, rent, payroll, and so on. The other is mission-based, spent on various initiatives. These expenses have to be accounted for separately.

The best fund accounting software must also have efficient budgeting features because it affects grant applications, pledges, gifts, and credit extensions. Plus, there’s the obvious need to keep costs in control and set spending limits. 

Payment automation

Automated, user-friendly, and flexible payment processing helps in two main ways. First, the process of receiving donations is streamlined. Tools like online donation forms and multiple payment methods add to donors’ convenience while reducing your workload. 

Second, it gets easier to pay your vendors and staff on time. If both incoming and outgoing payments are made more efficient, nonprofits can focus on their initiatives much better. 

Reporting and compliance

These features are available with varying degrees of customizability and granularity in most quality accounting solutions. However, in fund accounting software for municipalities, nonprofits, and religious organizations we are looking for some extras. 

The reports must be detailed enough to meet regulatory demands, for instance. They should allow evaluating performance against the budget and not just in terms of income and expenses given that the success of a nonprofit is measured through things such as fundraising ROI, donor and donation growth, program efficiency, etc. Some top fund accounting systems go beyond these features and even help prepare and file paperwork such as Form 990. 

CRM integration

It’s desirable to have your system for managing donor relationships synced with fund allocation, bookkeeping, and reporting. This optimizes your team’s efforts in building relationships with existing and potential donors.

Fund accounting software for municipalities, churches, and nonprofits does not always have built-in CRM, as it helps keep the cost low. However, in most of these cases, they might offer integration with a third-party CRM program. 

Ease of use and support

We have mentioned above that usability is a particularly important criterion for fund accounting systems, especially those meant for small organizations. We prefer software without a steep learning curve, designed for first-time users or those lacking accounting experience. 

On a related note, the kind of handholding provided by the product team also matters. Fund accounting software with multiple online resources and more extensive communication windows gets more points. Some top accounting software may provide dedicated support personnel, usually with upper tiers of their subscription plans, which is even more helpful.  


Apart from the many categories of features mentioned above, there are several other general aspects we consider. For example, there’s scalability—whether the subscription plans allow adding more features as the organization grows. Then, pricing is a critical factor in deciding the value an organization gets from any fund accounting software

Nonprofits often have full-time staff and volunteers working from home or remote locations. As a result, cloud-based fund accounting systems with mobile apps are usually more practical than desktop-based ones. The team’s work is also benefited if the software allows role-based access.

Customer reviews are another significant factor, which also helps get an idea of the quality of the support service. We go through feedback from past users of the software available at reputed review sites. If any specific negative aspects come up consistently in these reviews, we deduct points.

Reviews of The Best Fund Accounting Software 


Aplos is a feature-rich fund accounting system for nonprofits and churches that simplifies tasks like accounting, fundraising, and membership management. This easy-to-use and affordable tool caters best to small to medium-sized organizations and associations. 



The Aplos fund accounting system allows easy tracking of donations, grants, and special programs to keep your nonprofit prepared for financial reporting. Similarly, as efficient fund accounting software for churches, it simplifies the tracking of designated funds. The chart of accounts offers flexibility to suit your organization’s needs, while the reporting can be easily customized by project, campaign, or department. You get over 70 reports on aspects like grants received, budget by fund or purpose, donations by contact, lapsed donors, top donors, and more.

Unlike many accounting solutions, Aplos allows treating each fund as a separate entity, with its assets, liabilities, income, and expense records. While bookkeeping can be done at an organization level, many users appreciate this granularity.

Aplos also works as excellent fund accounting software for local government because of its stellar budgeting features. You get high-quality reports to compare budgets with actual expenditures. It’s also easy to budget over multiple years to ensure your programs are financially sound.

Donation reporting is made easier through pledge tracking and readily available information on donations by current and lapsed donors and other related aspects. Aplos also lets you track grants across programs and projects and generate reports on how much money has been used or is remaining. 

In fact, online donation tracking is largely automated in this fund accounting software, substantially reducing manual work. Churches can automate recurring giving and create customized and mobile-friendly donation forms or widgets to make it easier for people to donate. Online payments through WePay make it more convenient for donors to send money. Moreover, tax-deductible gifts are tracked according to the giver, saving substantial time when preparing statements for your donors.

The built-in CRM is excellent for improved relationship management with donors. Communication with donors is made more effective with customized templates, automation of recurring tasks, and prompts on how and when to send messages. This makes Aplos a valuable fund accounting software for churches and nonprofits.

There are event management functions, such as registration, ticket sales, and attendance tracking, to help raise more money. The Aplos subscription includes hosting fees for a website, while the website builder allows anyone to create a beautiful site without HTML knowledge.

The Aplos system includes a member portal with role-based access for members, volunteers, and your board. This helps streamline communication, schedule meetings, delegate tasks, and record minutes.

On the negative side, some notable factors may force you to check out other fund accounting software. At the time of writing, Aplos doesn’t have a mobile version, so its functionality, if you are away from the office, is limited. Its invoices offer little customizability. The payroll features are excellent but offered through the integration with Gusto, meaning you’ll have to spend more. Also costing extra are some useful features like text message donations and the addition of users.

Pricing: Aplos has three payment plans: Lite ($79/month), Core+ ($139/month), and Core & Advanced Accounting ($189/month + free demo). Annual subscriptions are at a 10% discount. Some features cost extra. Lite and Core+ plans include a free 15-day trial. 


FastFund is cloud-based fund accounting software for local government agencies, religious organizations, education and healthcare providers, nonprofits, and associations. While it packs a wide range of useful features, it scores a bit low on usability, especially for those with little prior experience with accounting software.



A unique aspect of FastFund by Araize is that the accounting, fundraising, and payroll modules can be subscribed to separately or bundled together. This allows substantial flexibility, and smaller organizations can cut their expenses on fund accounting software by paying only for what they need.

FastFund supports true fund accounting, meaning multiple funds can be set up as separate entities with their own trial balances and financial statements. Any inter-fund transactions automatically create a fund balancing entry, with a detailed audit trail printable for all fund balancing or source entries.

You can customize the chart of accounts to mirror your organizational structure. Data can be tracked across different segments like funds, programs, funding sources, and departments. Moreover, all your financial statements are FASB-compliant, with detailed reports possible for any time frame. FastFund is also handy for completing your IRS Form 990 and other documentation.

Budgeting is one of the components that make FastFund among the best fund accounting software products. It has features to create budgets according to fund sources and programs, create multiple budgets, generate comparisons, and automate budget creation from past years’ data. 

On the whole, we found the accounting module very comprehensive. You have the efficient entry of cash receipts and disbursements, automated recurring and reversing entries, custom financial statements, convenient bank reconciliations, and robust search functions. One area where FastFund could improve is its invoicing, but that’s not going to concern many users.

The fundraising module is designed to increase donations and cultivate long-term relationships. It works much like a CRM system in other fund accounting software for nonprofits and helps manage memberships, campaigns, constituents, and volunteers. You can also conveniently record all interactions with constituents and assign user-defined codes to different people. 

Educational organizations will like the handy alumni management feature, which makes it easier to approach alumni for donations and other assistance. There’s seamless credit card and ACH donation processing, tracking of donation designations, automated and customized receipts, along with competent reporting.

A valuable aspect across all modules is that these are designed by professionals with extensive experience working with nonprofits. Their familiarity with the sector’s specific financial challenges means you have customer support you can count on. 

The third module of this fund accounting software simplifies salaries and payroll taxes within your organization. It makes it easy to allocate these costs across grants and programs. You can customize pay types to account for any tax-exempt status, adjust for deductions and other factors, and even automate the payment of payroll taxes.

Apart from the average user interface, other negatives include the lack of a mobile app and the below-average customizability of reports. The cost of one-on-one training is not included in the subscription fee. So, if you plan on using all three modules, FastFund can prove more expensive than some other fund accounting software for municipalities, churches, and nonprofits. 

Pricing: FastFund Accounting has two plans: Standard ($42/month) and Premium ($94/month). For FastFund Fundraising, the Standard plan costs $42/month, while the Premium plan costs $82/month. FastFund Payroll’s price depends on the number of employees, with the lowest monthly fee of $66/month for 1 to 5 employees. Users can opt for a 30-day free trial or a free online demo.

QuickBooks Enterprise Nonprofit

Of all the QuickBooks products for nonprofits, QuickBooks Enterprise offers the best set of features for a growing organization. However, this software can be expensive, and users looking for simpler, more affordable, or cloud-based fund accounting software can evaluate QuickBooks Online. 



QuickBooks Enterprise Nonprofit offers several features specially designed for nonprofit and charitable organizations. These include the ability to add up to 40 users with individual permissions, store data on thousands of donors, and use advanced reporting for powerful insights. 

The fund accounting system allows categorizing expenditures by fund or program, while the chart of accounts can be customized to your needs into different accounts and subaccounts. Like other top nonprofit or government fund accounting software products, it also offers a unified chart of accounts for easy and reliable data transfer to IRS forms.

You can customize payment receipts for consistency across all donor communications. The Microsoft integration makes it easier to use a range of templates or create a new format from scratch for letters and other documents.

With bill and purchase order workflow approvals, you can better manage your cash flow and improve transparency by creating a digital audit trail for every transaction. Cash flow management and bill tracking can also be done from one dashboard, ensuring better control over your financials.

This fund accounting software for churches and nonprofits helps bill management further by the ability to schedule bills and pay them from within the system. You can easily choose the funding source and use the payment mode preferred by your vendor.  

To manage your various initiatives, you can easily create budgets by programs, compare them with actuals, and make adjustments as the need arises. With detailed statements on income and expenses, you know where every penny is going. It’s easy to figure out where your spending veers off course to correct it on time. Similarly, you also get fund-level balance sheets along with clear comparisons with prior years’ figures.

We particularly liked that this fund accounting software helps manage donor data no matter the size of your donor base. You can see contributions by each donor and grant, stay on top of communication, and ensure that donations keep coming. Among the many reports in the system, there’s also information on your biggest donors, which helps streamline your fundraising campaigns. 

A significant advantage of all QuickBooks products is their integrations catalog. With Enterprise Nonprofit, you have the choice of over 200 apps, including Method:Donor, Kindful, and DonorsFix. 

QuickBooks Enterprise is a desktop-based fund accounting system, but remote access can be bought at an additional price. This is part of the main problem we see regarding its suitability as fund accounting software for municipalities, nonprofits, and other bodies with monetary constraints. 

The base per-user cost is quite high, to begin with, and additional costs for cloud storage or extra users can quickly add up. Some plans also don’t include payroll and the Salesforce CRM connector either.

Pricing: QuickBooks Enterprise has three subscription plans. The per-user fees without remote access are $1,740/year (Gold), $2,140/year (Platinum), and $4,200/year (Diamond). Free trials are not offered, but potential users can contact the firm for a free online product tour. 

Oracle NetSuite

Better known as ERP software, NetSuite also works very well as a financial management and fund accounting software for nonprofits, faith-based organizations, and education and healthcare providers. While the product’s pricing is customized to users’ needs, most small and mid-sized firms are likely to find rival fund accounting systems more affordable.



Let’s begin with NetSuite’s core accounting features that consolidate all aspects like general ledger, accounts receivable and payable, cash management, allocation schedules, and real-time reporting within one system. Many processes related to journal entries, purchase orders, and vendor billing can be automated for improved productivity.

What makes NetSuite one of the best fund accounting software solutions is its GAAP- and FASB-compliant system. It simplifies managing different revenue streams, connecting revenue sources to expenses, and aligning with fund restrictions and grant requirements. As with other top fund accounting systems, the chart of accounts can be customized to meet your needs and have clear visibility into cash flow, fund balances, grant activity, and performance metrics. Greater control over your organization also comes with 250-plus standard and customized reports.

The grant accounting features in NetSuite are more advanced than other fund accounting software for local government agencies, nonprofits, churches, etc. You can track terms and conditions, automate time and expense tracking, and manage transactions with ease. Event management features allow tracking not just expenses but vendors, subcontractors, and employees associated with an event.

With one system managing funding source data from receivables and revenue transactions, your A/R aging, financial reporting, and reconciliation are simplified. GL segment combination codes can be set up easily to automate data entry of transactions against a grant. Other handy features include easy tagging of restricted revenue transactions, setting up billing schedules, and hassle-free searching for invoicing requirements by donor or grant.

For compliance with FASB requirements, you can remove the guesswork and cut down on manual effort through the built-in reporting of this fund accounting software. It is mapped closely to Form 990 line items but also offers sufficient customizability. 

NetSuite has several other valuable functions beyond core accounting. For instance, it has a KPI scorecard that uses governance metrics recommended by the watchdog agency Charity Navigator. Using this scorecard, you can align definitions of success across the organization and ensure sustained commitment to funding programs. 

The software is good for efficient tracking of individuals, organizations, households, relationships, and multiple revenue streams. The 360-degree view of all constituents helps manage and cultivate important relationships. You can establish customized workflows, segment constituents, manage email communication, and track related actions. While NetSuite’s fundraising and relationship management features are not as robust as some other fund accounting software for nonprofits, they can get a lot done for you.

NetSuite is designed for large organizations. As a result, it supports working from anywhere and lets you easily manage an organization spread across multiple locations on a unified platform. Features that help in this regard include a mobile app, strong data security, and support for multiple languages, currencies, and compliance standards.

Pricing: NetSuite does not disclose its pricing structure. Interested buyers can get in touch with the sales team for customized pricing. 

How to Choose the Best Fund Accounting Software for Your Organization

While all of the solutions featured on our list have enough features to cater to your nonprofit accounting needs, some would suit you better than others. That’s why we have also prepared a short guide to aid you in finding the best accounting solution for your organization, be it a faith-based organization, local government agency, association, or education and healthcare provider. 

Define Your Needs 

You should start by figuring out exactly what you want from the accounting solution. To do that, consider the needs of your organization. Is it a church, a nonprofit, a government agency, etc.? If you are running a faith-based organization, you could also consider using specialized church accounting products whose features sometimes differ slightly from those of fund accounting software

Then, how big is your organization and how many people would need access to the software? Do any of them work remotely? How large is your donor base and what is the size of your average donation? Do you get any grants and are your donations only monetary? Answering all these questions will help you list the features you need. 

Define Your Budget 

Once you have a list of features, determine a budget and check if any of the solutions with the features you need match it. If not, either tweak your budget or scrap some features. Last but not least, when planning your budget, remember that some fund accounting software come with cheaper annual plans, meaning that you could yield some savings by opting for a longer-term subscription.