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It’s the middle of grant season, and your team is buried in spreadsheets. Your board requests a quarterly financial report, but the information you need lives across your CRM, email threads, and a dozen Excel tabs. Hours later, after reconciling mismatched totals and verifying restricted versus unrestricted funds, you’re reminded that far too much is spent chasing down data.
Manual reporting and disconnected systems remain two of the biggest financial management hurdles for nonprofits, alongside the challenges of complex fund tracking. Together, these issues slow donations, weaken compliance, and make it harder to deliver accurate, timely information to donors and funders.
According to Salesforce’s Nonprofit Trends Report, 76% of nonprofits lack a formal data strategy—leaving finance teams without the visibility and tools they need to manage funds confidently or measure impact in real time.
As Marina Peterson, CFO of Downtown Streets Team, put it during a recent Accounting Seed discussion, “We have to keep up with the technology curve—especially in nonprofits. We need to rely on our systems and partners so we can do more automation and spend more time on our mission.”
Built for fund tracking, grant management, and donor transparency, today’s nonprofit accounting solutions help teams handle the financial drudgery, so they can focus on advancing their cause. Below, we compare leading nonprofit accounting software options and what to look for when choosing the best fit for your organization.
Using Salesforce? Jump ahead ↓
If your organization already uses Salesforce—or plans to adopt it—you can skip straight to our review of Accounting Seed. As the only solution in this list built natively on Salesforce (and fully integrated with solutions like the Nonprofit Success Pack, or NPSP) and NP Cloud, it connects your donor, financial, and program data in one unified platform.
Best Solutions for Small Nonprofits, Churches, and Volunteer-Run Organizations
These solutions prioritize affordability, ease of use, and quick setup—ideal for smaller teams or organizations without dedicated accounting staff.
Accounts by Software4Nonprofits
Accounts is a simple, low-cost accounting program tailored to small charities, churches, and clubs. The software provides true fund accounting with a customizable chart of accounts, budget creation and tracking, and automated nonprofit reports like fund-specific income statements. Available as a desktop version for Windows or an OnDemand cloud version usable on Mac or PC. Setup can be completed in hours, and the system allows managing up to five separate organizations’ books. An optional Donor Management companion program (Donarius) is available for tracking donors and contributions.
Best for: Very small nonprofits, volunteer-run organizations, or groups with shoestring budgets that still need proper fund accounting
Limitations: Basic feature set, desktop version is single-user, and there is limited scalability for growing organizations
Aplos
Aplos combines fund accounting with donor management and online giving in one cloud-based solution. The software tracks restricted versus unrestricted funds, manages donations, generates contribution statements, and produces financial reports. Because it includes both accounting and fundraising tools, organizations can handle finances and donor relationships without switching between systems. Aplos uses simplified terminology instead of traditional accounting language, which helps non-accountants navigate the system.
Best for: Churches and small to midsize nonprofits looking for an all-in-one solution
Limitations: May lack advanced features that larger, more complex organizations require; users report customization can be limited
QuickBooks Nonprofit Edition
QuickBooks is widely used general business accounting software with a Nonprofit Edition that adds donation tracking, grant management, and fund-specific reporting templates. The solution handles bank reconciliation, expense tracking, budgets, invoicing, and can generate financial statements for board meetings. Users can accept donations through multiple payment methods and access over 750 third-party integrations, including nonprofit-specific solutions like Kindful and DonorPerfect.
Best for: Small nonprofits with straightforward accounting needs and in-person teams
Limitations: While QuickBooks can be customized for nonprofits, it lacks the functionality of a dedicated donor CRM. It is limited to basic contact management, with comprehensive CRM capabilities, advanced fund accounting, and specialized training all requiring premium integrations and additional fees. In addition, reviews indicate remote access to QuickBooks costs extra, posing a challenge for a growing number of remote and hybrid nonprofit teams.
Xero
Xero is cloud-based general business accounting software that includes invoicing, bank reconciliation, expense tracking, and payroll capabilities. Nonprofits can track donations and grants, generate financial reports for boards and donors, and manage cash flow through a real-time dashboard and mobile app. Xero offers a 25% discount to registered nonprofits and provides automated payroll that supports federal and state requirements. Organizations can extend functionality by connecting over 1,000 third-party apps from the Xero App Store, including nonprofit-focused CRM tools like Keela (donor management and fundraising analytics), Infoodle (volunteer and donor engagement), and Hubdoc (automated bill and receipt imports).
Best for: Small nonprofits comfortable with general accounting software and willing to add integrations for specialized needs
Limitations: Requires third-party app integrations to handle fund accounting, restricted fund tracking, donor management, and nonprofit-specific compliance reporting.
Best for Mid-Sized Nonprofits with Complex Grants or Compliance Needs
These systems support deeper fund accounting, donor reporting, and FASB compliance—ideal for organizations with dedicated finance staff, multiple grants, or restricted funding streams.
Fund EZ
Fund EZ is a nonprofit-specific accounting solution focused on ease of use. The software supports fund accounting with budget tracking across multiple projects or grants and produces standard nonprofit financial statements. Available as a cloud-based solution or on-premise installation, Fund EZ includes features like general ledger, bank reconciliation, accounts payable and receivable, and client billing. Advanced features like purchase orders, indirect allocations, and dashboards require the Fund EZ Pro version.
Best for: Small to midsize nonprofits that prioritize simplicity and quick implementation
Limitations: Users say report customization can be labor-intensive and time-consuming and budget setup operates at a global level, making individual budgets difficult to configure
GMS (Grants Management Systems)
GMS is built specifically for grant-driven nonprofits, integrating core accounting functions with specialized grant tracking. The system handles general ledger, accounts payable, payroll, and provides tools for tracking grants, contracts, and program activities. It meets FASB 116/117 compliance requirements and includes cost allocation features for grant reporting.
Best for: Nonprofits heavily reliant on grant funding with complex compliance requirements
Limitations: No donor management or fundraising features available, difficult to customize reports (all reports created as PDF); limited third-party integration (only imports/exports via Microsoft Word, Excel, or CSV)
MIP Fund Accounting
MIP provides comprehensive fund accounting and grant management designed specifically for nonprofits and government entities. The system includes general ledger, budgeting, grant tracking, and reporting with FASB and GASB compliance built in. MIP’s modular design allows organizations to add payroll, HR, and other modules as needed. The solution supports managing multiple funds, tracking restricted donations, and generating detailed financial statements that meet nonprofit reporting standards.
Best for: Small to mid-sized nonprofits focused on fund and grant accounting with strong compliance requirements
Limitations: Users report the system is not intuitive and has a steep learning curve with insufficient training resources and lacks integration capabilities with other systems. They also note the interface feels outdated and navigation can be confusing.
Cougar Mountain (Denali Fund)
Available on-premise or in the cloud as Denali Fund, Cougar Mountain offers nonprofit accounting with strong audit trail capabilities. The software includes modules for general ledger, accounts payable and receivable, and payroll. Organizations can create custom financial reports and set up automatic backups. Optional add-ons provide donor management and fundraising functionality.
Best for: Nonprofits that need scalable accounting with detailed audit trails and GAAP/FASB compliance
Limitations: Users report the budget module can be difficult to enter data and set up, dashboards and multiple solution integrations are lacking, help guides lack sufficient detail, and there can be issues with the remote app due to firewall problems.
NonprofitPlus
This cloud-based ERP suite runs on Acumatica and provides fund accounting, budget controls, and grant management. Modules cover general ledger, accounts payable and receivable, encumbrance accounting, and even board and volunteer tracking. Organizations can manage restricted funds, generate comprehensive reports, and scale through customizable modules as they grow.
Best for: Growing nonprofits that need ERP-level functionality with room to scale
Limitations: Users say it can be expensive compared to other solutions, calculation processing slows down with large amounts of account data, and it requires proper training to operate effectively due to exposure to multiple modules.
Already on Salesforce? This one’s for you
If your nonprofit runs on Salesforce—or is considering it—you’ll want to head straight to our review of Accounting Seed. It’s the only accounting platform in this list built directly on Salesforce, meaning your donor data, financials, and program details live in the same system—no connectors, no duplicate entry, no data gaps.
Best for Large or Multi-Entity Nonprofits with Enterprise Needs
Enterprise-grade solutions designed for multi-location operations, complex program structures, and large-scale fund management.
Blackbaud Financial Edge NXT
Built for nonprofits, Financial Edge NXT provides fund accounting, grant tracking, budgeting, and strong internal controls with comprehensive audit trails. The solution integrates with Blackbaud’s donor CRM and fundraising tools, creating a unified ecosystem for organizations already using Blackbaud products. The system supports FASB compliance, multi-dimensional reporting, and automated account reconciliation.
Best for: Established nonprofits requiring nonprofit-specific features and tight integration with Blackbaud fundraising and donor management tools
Limitations: New users may find the system complex with a learning curve, limited integration with non-Blackbaud products and APIs not fully developed, performance can be slow at times, and export functionality defaults to older Excel format.
Oracle NetSuite
NetSuite is a full ERP suite with nonprofit editions that include core accounting, fund and grant management, CRM, and e-commerce capabilities in one solution. The system offers customizable dashboards and workflows, multi-currency support, and real-time financial visibility. NetSuite can handle complex, global operations with features like automated revenue recognition and consolidation across multiple entities. Oracle offers the Social Impact program with special pricing for qualifying nonprofits.
Best for: Medium and larger nonprofits with complex operations or global needs requiring an integrated, scalable ERP solution
Limitations: Users say implementation can be costly and time-consuming, requires a dedicated NetSuite architect or power user to maximize functionality, interface described as cumbersome and non-intuitive by some users, and customization changes can be slow and expensive. For organizations on Salesforce, integration requires third-party connectors like Celigo or Boomi rather than native connectivity, which can lead to data sync delays and integration issues.
Serenic Navigator
Serenic Navigator (now part of SylogistMission) is an enterprise-level solution built on Microsoft Dynamics 365 Business Central. The software provides fund accounting, budgeting, multi-currency support, and compliance features for nonprofits and governments. It includes accounts payable with automated workflows, general ledger automation with customizable dimensions for tagging transactions, and accounts receivable with customizable invoice templates. The solution also supports fundraising, donor management, and grant processes in one system, linking accounting with donor tracking and reporting.
Best for: Large nonprofits and international NGOs needing enterprise ERP capabilities with donor management
Limitations: Users report the system has a learning curve. Some reviewers note the GUI could be improved and that client work isn’t always proactive, and that report formatting (particularly printing forms) and limited data analysis tools are areas of concern.
Sage Intacct
Sage Intacct is a cloud-based financial management platform with specialized nonprofit editions that include fund accounting, grant tracking and billing, revenue recognition, and outcomes reporting. The solution offers real-time reporting, role-based dashboards, and AI-powered automation through Sage Copilot. The system includes dimensional general ledger capabilities that allow organizations to view their data from multiple perspectives. Sage Intacct offers two nonprofit plans: Standard (for established small and mid-size organizations) and Premium (for larger, more complex organizations with advanced reporting needs).
Best for: Established mid-sized to large nonprofits seeking comprehensive financial management with fund accounting, grant tracking, and advanced reporting capabilities
Limitations: Users report that pricing has increased significantly in recent years. Some reviewers note that certain functions like AP, payroll, and fixed assets lag behind specialized third-party software. The system has a learning curve and some users also note limitations in customization capabilities and approval workflow options. For organizations on Salesforce, Sage has a pre-built integration—but it can require frequent maintenance and result in data sync delays or data inconsistencies.
Tangicloud Fundamentals
Tangicloud Fundamentals is a fund accounting and ERP solution built on Microsoft Dynamics 365 Business Central, designed for nonprofits and governments. The solution offers unlimited funds with automatic due-to/due-from transactions, budgetary control with spending alerts, and paperless approvals. Features include grant management that tracks awards, expenditures and indirect cost recovery, real-time budget availability viewing, and flexible bank accounts for handling multiple funds and currencies. The system integrates with Microsoft Office products including Excel, Word, and Outlook for familiar workflows.
Best for: Nonprofits and government organizations already invested in the Microsoft ecosystem needing comprehensive fund accounting with modern ERP capabilities
Limitations: Users say formats require manual intervention, especially on Mac (only works via Excel downloads), budget setup and comparison can be complicated, and using the solution requires understanding of the software’s administrative backbone to ensure correct operation.
Best for Salesforce-Based Nonprofits Seeking a Unified Platform
For nonprofits that already rely on Salesforce—or plan to adopt it—you need a native solution to unify financial, donor, and operational data within the Salesforce ecosystem.
Accounting Seed
Accounting Seed runs natively on Salesforce, giving nonprofits a unified platform where donor information, financial data, and program details live in the same database. Because it’s built on Salesforce rather than bolted on through integrations, donations entered in the Nonprofit Success Pack (NPSP) and NP Cloud flow directly into the general ledger—automatically categorized and audit-ready.
The platform handles fund accounting with self-balancing ledgers for each fund or program, tracks restricted and unrestricted donations, and manages grant lifecycles from donor intent through audit reporting. AR and AP automation reduce manual data entry, while customizable dashboards provide real-time insights into financial health, donor engagement, and program effectiveness.
Organizations like Baptist Global Response use Accounting Seed to track up to 300 programs simultaneously, applying specific donations to individual projects with complete visibility from donation to outcome. Downtown Streets Team cut bank reconciliation time from two days to two hours and discovered $100,000 in previously unbilled expenses within 90 days of implementation.
Best for: Nonprofits already using Salesforce or planning to adopt NPSP who want accounting and CRM data in one platform
Limitations: Requires Salesforce as the underlying platform—though for many nonprofits, that’s a benefit. As the world’s leading CRM, Salesforce provides built-in donor management, automation, and security features that make Accounting Seed’s native connection especially powerful. Nonprofits not yet using Salesforce will need to implement it first to take full advantage of the platform’s unified data model and automation capabilities.
Real results at Downtown Streets Team
For Downtown Streets Team—a California nonprofit helping unhoused individuals gain stability through work and community—modernizing accounting meant gaining control of their finances. When Peterson joined as CFO, financial statements were outsourced and arrived 60 days late. With Accounting Seed on Salesforce, her team brought accounting in-house, shortened their close to ten days, and uncovered $100,000 in previously unbilled expenses within 90 days.
“What used to take two days in Excel takes two hours in Accounting Seed,” said Peterson. “Now my team can focus on spending contracts correctly, revising budgets when needed, and partnering with our program directors to make smarter financial decisions.”
Peterson also highlighted how automation reshaped her team’s impact: “Our accountants need to be more than high-skilled data entry now. Automation helps them become analysts and partners in the work instead of just processors.”
Choosing the right nonprofit accounting solution
For nonprofit leaders, the right accounting solution isn’t just about keeping the books balanced—it’s about accountability, transparency, and impact. Your system should make it easy to track restricted and unrestricted funds, automate grant and donor reporting, and produce real-time insights you can share confidently with your board and funders.
Look for software that can adapt to your workflows rather than forcing you to adapt to it. A strong solution should:
- Support true fund and grant accounting that complies with FASB and donor restrictions.
- Connect seamlessly with your donor CRM data to keep financial and relationship data in one place.
- Automate key processes like bank reconciliation, expense allocation, and reporting.
- Provide flexible dashboards so teams can see the financial health of every program at a glance.
That’s where Accounting Seed stands out. Built natively on Salesforce and fully connected with the Nonprofit Success Pack (NPSP) and NP Cloud, it brings your financial and donor data together in a single system. With automation for AP, AR, and grant tracking—and customizable reports that meet each funder’s requirements—nonprofits gain accuracy, visibility, and confidence in every dollar spent.
As Shannon Canzanella, manager at Accounting Seed expressed in a recent discussion: “It’s about bringing accounting and finance out of that dark back office and into every room of the building—making them strategic partners in every decision.”
If your organization is ready to move beyond spreadsheets and manual reconciliations, Accounting Seed delivers the unified, audit-ready solution you need to focus less on data gathering—and more on driving your mission forward.
In the words of Peterson: “Enter data once and use it often. Every accountant should write that on a Post-it and live by it.”
Ready to see what accounting built for nonprofits looks like in action? Schedule a personalized demo to explore how Accounting Seed on Salesforce can simplify your fund tracking and reporting workflows.
See Accounting Seed in action
See how accounting on Salesforce can eliminate the need for costly integrations—and silos of mismatched information—by sharing the same database as your CRM.
