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Top Rated Nonprofit Accounting Software with Payroll management - Page 2

Last updated: October 2026

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39 software options

Denali Fund logo

Nonprofit accounting software

Denali FUND by Cougar Mountain Software is a cloud-based and on-premise accounting software designed specifically to help nonprofit organizations streamline & manage all accounting processes, including accounts payable & receivable, general ledger, bank reconciliation, payroll, and more

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AccuFund Accounting Suite logo

Online and Onsite Accounting Software for Nonprofits & Govt

AccuFund’s complete nonprofit financial management system improves all critical aspects of your nonprofit, from budget development to grants management to payroll and HR and accounts payable, selecting the modules that your nonprofit needs now and add others in the future as needs evolve.

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Aptean Industrial Manufacturing ERP Traverse Edition logo

Discrete manufacturer ERP with mobile access and automation

Aptean Industrial Manufacturing ERP Traverse Edition is an ERP software tailored for discrete manufacturers. The solution is built on Microsoft technologies, providing businesses with a customizable platform that integrates with a variety of tools including Aptean Ship, Aptean Pay, and BI for real-time data analytics and decision-making.

Read more about Aptean Industrial Manufacturing ERP Traverse Edition

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Accounting Seed logo

Accounting and analytics software built on Salesforce

Accounting Seed is an accounting application built natively on Salesforce. Its customizable, enabling users to manage their accounting their way. As a full accounting solution, Accounting Seed tracks financial data through the entire business lifecycle.

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SylogistMission ERP logo

Fund accounting solution for non-profit organizations.

Serenic Navigator for NPO is a cloud-based and on-premise fund accounting solution which helps non-profits manage resources, programs, and finances on a unified platform. It allows users to have complete visibility into the budgets and expenditures required to manage funding sources and programs. The software delivers several functions including donor management, payroll processing, human resources, budget tracking, grant management, encumbrance, and more.

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Xero logo

Cloud-based accounting software for small businesses

Xero is an award-winning online accounting software designed for small business owners and accountants, available on any computer or mobile device with an internet connection. Simplify business admin and get a range of financial insights to help you make better decisions for your business.

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MNprogram logo

Sales management software for legal and medical industries

MNprogram is a cloud-based system designed to help businesses in legal, medical, healthcare, and other industries manage sales, customers, billing, accounting, and more. It enables supervisors to automate employee scheduling, run marketing campaigns, and store documents in a centralized repository.

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NetSuite logo

AI-powered cloud-based business management suite

NetSuite's ERP provides one integrated, cloud solution to manage your entire organization and accelerate your mission. Gain efficiencies with a powerful nonprofit fiscal management system built to meet the unique needs of your nonprofit.

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QuickBooks Online logo

Accounting and business management software

QuickBooks Online is an all-in-one online business software designed to help manage business finances. The platform is built to scale businesses, unlocking insights and providing the functionality of a larger team, all on one integrated platform.

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MYOB Business logo

Online accounting & payroll for every business

Small Business cloud based accounting software to automate payroll, manage financial performance, tax and all your accounting needs.

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Sage Accounting logo

Accounting software for small businesses

Sage Accounting is an accounting system for small business owners. It has features to help users forecast their cashflow, send and track invoices and act on real-time reporting. Users can manage their business from anywhere, at any time, from the cloud and with mobile functionality. Sage Accounting application is available for iOS and Android.

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CenterPoint Fund Accounting logo
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Affordable fund accounting for nonprofits.

Fund accounting for nonprofits with a price tag that won't break your budget.

CenterPoint Fund Accounting Software is a versatile and affordable fund accounting software and payroll software system that gives you the tools you need to take total control of your nonprofit financial management.

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Elexio Church Accounting logo
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Finance management software for churches and nonprofits

Elexio Church Accounting helps churches, ministries, and nonprofits manage payroll, online donations, memberships, and more. The built-in digital ledger lets users update journal entries, view data using drill-down capabilities, and create and store financial records in a centralized repository.

Read more about Elexio Church Accounting

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Macompta.fr logo
(0)

French-language accounting, invoicing & collection solution

macompta.fr is a modular accounting, invoicing & collection web-based solution. It is aimed at entrepreneurs, small businesses and associations based in France.

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