Best Fund Accounting Software for Higher Education Institutions and Foundations

Best Accounting Software for Higher Education Institutions and Foundations

At higher-education foundations and institutions, accounting work rarely fits into neat buckets. In a single day, you might track spending on a multi-year grant, release scholarship funds with strict conditions, document the use of an endowed gift, and prepare reports for a committee.

Fund accounting was built for this environment. You need software that can follow each fund from start to finish, keep spending aligned with the original purpose, support audits, and give departments the information they need without extra cleanup. You also need systems that work well with advancement, admissions, or donor engagement platforms so financial data isn’t being rebuilt by hand.

This roundup highlights accounting solutions that address these everyday pressures. Whether you support a university foundation, coordinate scholarships across colleges, or handle financial oversight for an education-focused nonprofit, these solutions are designed to help you keep the work accurate, organized, and clear to anyone who needs to review it.

Fund Accounting Systems Built for Education & Nonprofits

These tools support fund accounting without the weight of a full ERP and are well suited for colleges, departments, and education nonprofits that manage grants, scholarships, and donor-restricted funds. They balance structure with flexibility and help teams keep fund activity organized across programs.

AccuFund

AccuFund is a fund accounting solution built specifically for nonprofits, government entities, and community organizations that need detailed control over funds, grants, programs, and departments. It offers both browser-based cloud and on-premise options, along with modules for AP, AR, payroll, purchasing, fixed assets, allocations, grants, and timekeeping. Its document imaging and customizable reports give finance teams visibility into fund and grant activity while maintaining clear, auditable records.

Best for: Mid-sized nonprofits, government agencies, and organizations with multiple funds or grant cycles that need stronger controls and reporting than QuickBooks-level tools. A good fit for teams that want configurable fund accounting, integrated modules, and audit-friendly reporting, and who can support a more robust system.

Limitations: Reviews mention that report writing can be difficult to learn, exports to Excel can be limited, and budgeting tools can feel clunky. Some users note occasional issues after upgrades, a time-entry module that’s harder to use, and cloud performance that varies.

Aplos

Aplos is fund accounting software built specifically for nonprofits, churches, and small foundations that need simple tools to track funds, donors, and programs in one place. It offers true fund accounting, FASB-friendly reporting, donor management, online giving, and basic CRM features. Users like its ease of use, clear navigation, and ability to manage contributions, budgets, and financial reports without an accounting background. Bank connections, transaction entry, and reconciliation are straightforward, and many appreciate the built-in training and responsive support. For smaller organizations, Aplos often replaces tools like spreadsheets or QuickBooks by providing an accounting structure that follows nonprofit terminology and makes it easier to separate restricted and unrestricted funds.

Best for: Small to midsize nonprofits, churches, community organizations, and foundations that want simple fund accounting, donor tracking, and online giving in one tool—without needing ERP-level complexity. Ideal for teams without formal accounting staff who need clear reports and an easy way to manage restricted funds.

Limitations: Reviews mention limited integrations, a CRM that lacks more advanced donor-management features, and occasional bugs in reporting filters.Some users want more flexible reporting or automated workflows, and a few note that features are split across higher-tier plans.

Blackbaud Financial Edge NXT

Financial Edge NXT is Blackbaud’s cloud accounting system built for higher education institutions and nonprofit organizations that need fund accounting, accessible reporting, and audit trails. It gives finance teams access to budgets, activity, and reports from anywhere, which helps faculty and administrators review financial details without digging through database tools. Institutions can use it to manage grants, track spending across programs or departments, and build reports that support board reviews, research activity, or operational planning. Integrations with other Blackbaud products—especially Raiser’s Edge—are a core appeal for schools that rely on a shared ecosystem for fundraising, donor activity, student payments, and financial records.

Best for: Higher education institutions and education-focused nonprofits that already use other Blackbaud products or want a fund accounting system that supports grants, departmental budgeting, and board-ready reporting. Works best for teams that need an accessible cloud interface and value tight alignment with Raiser’s Edge and Blackbaud’s broader ecosystem.

Limitations: Users report slow loading times, limited flexibility in journal entry workflows, and frequent frustration with error handling. Integrations outside the Blackbaud ecosystem can be difficult, imports may require extra steps, and customer support responsiveness varies. Some screens still rely on switching back to the older database view.

BUCS (Frey Municipal Software)

BUCS is a true fund-based accounting system built for government entities, utilities, and nonprofits that need strong budget controls, compliant reporting, and real-time processing. The system supports a 29-digit customizable chart of accounts, tight budget enforcement, allocation posting, encumbrances, and detailed audit trails. Financial statements can be customized or exported to Excel or Crystal Reports, and modules can be added as needs grow.

Best for: Small to mid-sized governments, utilities, and nonprofit entities that need real fund accounting with strong budget controls, multi-fund tracking, and integrated modules for AP, payroll, utilities, and HR. Best for teams wanting an easy-to-learn system backed by hands-on support rather than a large ERP environment.

Limitations: Users say that report creation can be confusing and entirely user-built, increasing the chance of missing fields. Some mention strict user-count limits that require resets, certain screens that feel dated, and add-ons that raise costs. A few reviewers want easier vendor searches and more flexible reporting defaults.

Fund E-Z Development Co

Fund EZ is nonprofit fund accounting software built for organizations that need clear tracking across programs, grants, departments, and funding sources. It offers an easy-to-learn interface, flexible account structures, and strong reporting options that export to Excel. Fund EZ supports budgets, AP, AR, allocations, client billing, and encumbrances, with optional modules for fundraising, fixed assets, Medicaid billing, foster care billing, and more. It’s designed for nonprofits that want straightforward fund accounting without the cost or complexity of larger ERP systems.

Best for: Small and midsize nonprofits with multiple programs or funding sources that want an affordable, easy-to-use fund accounting system. Ideal for teams upgrading from QuickBooks who need fund-specific reporting and drill-down visibility without managing a full ERP.

Limitations: Reviews note that budgeting tools lack flexibility, custom report building can be time-consuming, and some version upgrades introduce new quirks. Users also mention limited built-in help, fixed asset constraints, and the need to know exact date ranges for accurate multi-fund reporting. ACH functionality has been slow to arrive.

MIP Fund Accounting

MIP Fund Accounting is built for nonprofits, government entities, and education institutions that manage multiple funds and revenue streams. Colleges and universities use it to handle tuition and fee activity, grant funding, donor support, and departmental spending across areas like instruction, research, and student services. Its segmented chart structure gives finance teams control over fund tracking, while dashboards and real-time expense views make it easier to follow budgets and audits. Institutions can deploy MIP in the cloud or keep it on-premise. Many choose it for its long history in fund accounting and for modules that cover payroll, purchasing, fixed assets, and other core needs.

Best for: Higher education institutions and nonprofit campuses that handle many restricted funds or grants and want a system built around fund accounting rules. Works best for teams that need strong control over segments and accounts and prefer a solution with a long track record in education and public-sector finance.

Limitations: Users mention a dated interface, a steep learning curve, and reporting tools that can feel rigid. Cloud customers often cite higher costs, slow performance, and extra fees for configuration changes. Support quality varies, and some institutions note inconsistent training resources and challenges during migrations.

Enterprise-Level ERP & large-institution solutions

These systems are built for universities, public institutions, and foundations that manage complex operations, multiple entities, and wide-ranging reporting needs. They offer extensive configuration options and handle large volumes of activity across programs, departments, and campuses.

NetSuite

NetSuite’s nonprofit accounting suite brings fund accounting, grant oversight, donor activity, and core financials into one cloud solution. Education foundations and nonprofit institutions use it to track restricted and unrestricted funds, monitor grant budgets, and tie donations, program costs, and in-kind gifts directly to the general ledger. Custom segments allow teams to tag activity by fund, program, grant, or donor restriction, making it easier to meet FASB and Form 990 reporting needs.

Best for:
Education foundations, midsize nonprofits, and multi-entity organizations that need fund accounting, donor tracking, and grant management in one system. A good fit for large teams already committed to the NetSuite ecosystem that can support a configurable ERP and want real-time visibility across programs, funding sources, and operations.

Limitations: Users report slow performance as data volume grows, rigid or confusing reporting tools, and difficulty extracting data due to similar fields and IDs. Customization often requires technical expertise, and integrations outside of the NetSuite ecosystem can behave inconsistently.

Sage Intacct

Sage Intacct is a cloud-based accounting solution that can be tailored to educational organizations—schools, colleges, libraries, associations—that have multiple locations or entities and diverse funding sources. It automates core workflows like approvals, consolidations and revenue recognition, supports GAAP-compliant financial statements and Form 990 submissions, and enables more than 150 standard reports plus user-built dashboards for visibility across funds, programs and stakeholders.

Best for: Education foundations or nonprofit arms of institutions with multiple entities, fund streams, or programs; who need deep reporting capabilities, multi-entity consolidation, and tight integration with donor, tuition, or student systems—and can support a complex implementation.

Limitations: Costs rise when adding advanced modules or integrations. Users often point to a steep learning curve, rigid editing of posted entries and mixed experiences with vendor support.

SAP S/4HANA Cloud (Fund Accounting for Higher Education & Public Sector)

SAP S/4HANA Cloud Public Sector Management (PSM) provides fund-based budgeting, grant administration, and revenue-expenditure control for public institutions, nonprofits, universities, and similar organizations. The PSM bundle includes Budget Management for enforcing budget rules, Grantee Management for sponsored research and grant activity, and Fund Accounting for GASB-aligned reporting across funds and fund areas. These components tie into Financial Accounting, Controlling, and Project System to support budgeting, spending checks, grants planning, invoicing, and fund-level statements.

Best for: Universities, higher-education foundations, public institutions, and large nonprofit organizations with complex fund, grant, and budget oversight requirements. A good fit for teams that must follow GASB or fund-based reporting rules and need unified finance, budgeting, grants, and procurement in one system. Works best for organizations with established IT resources and the budget required for an enterprise-level ERP.

Limitations: Reviews mention limited flexibility in certain workflows, slow performance with large data volumes, and a heavy reliance on external tools for advanced analytics. Licensing is costly, and customization often requires consulting support.

Small-organization cloud accounting solutions

These solutions fit smaller schools, programs, and foundations that need basic accounting, budgeting, and reporting without extensive setup. They work well for teams with limited staff or simpler funding structures who still want reliable day-to-day financial tracking.

QuickBooks Online

QuickBooks Online is a widely used cloud accounting solution that many schools, colleges, and small education programs choose for its ease of use and accessible design. It helps teams handle tuition and fee activity, track expenses, create invoices, and manage cash flow without a complex setup. Schools can build simple reports for administrators, monitor budgets, and use the mobile app to check finances from any device. Bank feeds pull in transactions automatically, and the system connects with hundreds of third-party apps for scheduling, payments, or payroll. Because many accountants already work in QuickBooks, institutions often pick it for easy collaboration and quick onboarding—even when they don’t have dedicated accounting staff.

Best for: Smaller schools, programs, and education nonprofits that need basic accounting, invoicing, and cash-flow tracking in a tool that’s quick to adopt. A good fit for institutions without formal fund accounting requirements or those that want something simple their outside accountant already supports.

Limitations: Lacks true fund accounting, segment tracking, and multi-entity structure. Reviews mention feature gaps compared to desktop versions, frequent interface changes, subscription price hikes, glitches with bank syncing, and inconsistent customer support. Some users say reporting and permissions are limited for more complex needs.

Xero

Xero is a cloud-based accounting solution often used by small and midsize nonprofits that want simple, accessible financial tracking without a complex fund-accounting system. Organizations use it to record donations and grants, manage expenses, run payroll, and view real-time cash flow from a clean dashboard. Reporting tools make it easy to generate statements for boards and funders, and the mobile app helps staff review budgets, approve payments, and reconcile bank activity from anywhere. Xero doesn’t handle true fund accounting on its own, but nonprofits can add donor and fund-tracking through connected apps such as Keela, Infoodle, and ApprovalMax.

Best for: Small nonprofits, community groups, and education foundations that need simple accounting, payroll, and reporting in an easy-to-use cloud tool. A good fit for teams without specialized finance staff, especially when paired with a donor or fund-tracking app to cover nonprofit-specific needs.

Limitations: Xero lacks native fund accounting, restricted fund tracking, or grant management without third-party apps. Reviews note that report customization is limited, invoices and imports can require workarounds, and advanced budgeting or allocations may feel basic. Integrations solve some gaps but add cost and setup time.

Salesforce-native accounting

This category includes accounting software built directly on Salesforce, allowing finance, advancement, and program teams to work from the same system. It’s the best option for institutions that already use Salesforce for donor activity, admissions, or student engagement and want accounting data to live in the same environment.

Accounting Seed

Accounting Seed is a Salesforce-native accounting platform used by schools, higher-education organizations, education foundations, and nonprofits that want fund and grant tracking inside the same system they use for admissions, fundraising, donor management, and community engagement. Because it’s built directly on Salesforce, Accounting Seed sits within the same system as NPSP/Nonprofit Cloud, Education Cloud, and Experience Cloud, letting teams tie financial data to CRM records without integrations or data sync issues. Admissions, advancement, program, and finance teams all work from one shared database, which reduces manual entry and provides real-time visibility into budgets, grants, tuition billing, donations, and departmental spending.

Organizations can allocate funds across programs, automate billing and receivables, and customize workflows using Salesforce automation tools. A multi-dimensional chart of accounts lets teams track transactions across funds, programs, departments, and other dimensions without the digit-count limits found in traditional fund accounting systems. Detailed reporting gives leaders insight into program costs, grant balances, and multi-department budgets, while AI-powered tools help reduce repetitive work. For colleges and multi-entity education networks, the platform supports complex structures, multi-currency, and multi-ledger accounting. When paired with NPSP or Nonprofit Cloud, Accounting Seed provides a complete CRM-to-financials environment that many education organizations use to replace disconnected systems and spreadsheets.

Best for: Education foundations, higher-education institutions, schools, and education nonprofits already using Salesforce—or planning to consolidate CRM and finance onto one platform. Ideal for teams needing real fund and grant management, automated billing, and flexible reporting that aligns with NPSP, Education Cloud, and Experience Cloud–based donor, student, or community workflows.

Limitations: Requires use of Salesforce, which may not be the right fit for institutions without an existing Salesforce footprint. But for schools, universities, and education nonprofits already using Salesforce for admissions, advancement, advising, or donor management, the native integration removes the friction common with bolt-on accounting tools and creates a unified, far easier operating environment.

Selecting the right solution for your foundation or institution

Accounting teams in education and nonprofit manage activity that shifts throughout the year and rarely follows the same pattern. Grants move on their own timelines. Scholarship spending rises and falls by term. Donor support can require careful documentation long after the gift arrives. The right software should help you keep these pieces organized, make reviews easier, and reduce the amount of cleanup you do behind the scenes. When the system fits your workflow, it becomes easier to give departments and leadership what they need without extra steps.

If your institution already uses Salesforce—or plans to bring finance and CRM work together—Accounting Seed offers a way to manage funds, grants, billing, and reporting in the same place your teams already work. You can request a demo to see how it fits your structure.