Best Nonprofit Software for Paychex Flex

Compare the Top Nonprofit Software that integrates with Paychex Flex as of February 2026

This a list of Nonprofit software that integrates with Paychex Flex. Use the filters on the left to add additional filters for products that have integrations with Paychex Flex. View the products that work with Paychex Flex in the table below.

What is Nonprofit Software for Paychex Flex?

Nonprofit software is a type of technology used to help nonprofit organizations manage operations more efficiently. It often includes features such as financial tracking, donor management, and project management tools. This software can be an invaluable resource for non-profits, enabling them to stay organized and achieve their goals with ease. Compare and read user reviews of the best Nonprofit software for Paychex Flex currently available using the table below. This list is updated regularly.

  • 1
    Sage Intacct

    Sage Intacct

    Sage Intacct

    Sage Intacct offers nonprofit organizations a financial management platform that supports fund accounting, grant tracking, and donor reporting. It provides customizable dimensions to track funds, programs, and projects separately for transparency and compliance. Automated workflows simplify grant allocations, expense approvals, and donor restrictions management. Real-time dashboards offer visibility into budget vs. actuals, fund balances, and revenue sources. The system integrates with fundraising and CRM platforms for consistent donor and financial data. Audit trails and role-based permissions ensure governance and regulatory compliance. Sage Intacct supports multi-entity consolidations for organizations with complex structures. It empowers nonprofits to maximize resource utilization and demonstrate accountability to stakeholders.
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  • 2
    Xero

    Xero

    Xero

    Save 90% for 4 months on Xero's award-winning accounting and online bookkeeping platform for businesses of all sizes and stages of growth. Beautifully simple, Xero covers a wide range of features that help businesses manage their finances effortlessly, including invoicing, inventory, bank connections, payroll, reporting and more. Xero also offers users free online support 24/7. Xero offers a robust ecosystem of connected apps and integrations with banks and financial institutions, enabling small businesses to access a wide range of solutions within Xero's open platform to streamline operations and manage finances. Additionally, accounting and bookkeeping firms benefit from efficient compliance tools, advanced practice management software, and a cloud-based unified accounting ledger for all clients, centralized in one place.
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    Starting Price: $20/month
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  • 3
    DATABASICS Time & Expense
    DATABASICS is driven to meet the most demanding Time and Expense management challenges for mid- to large-size enterprises with distributed workforces around the world. By combining two world-class tracking systems in one, we address two critical business processes with absolute ease in one solution. Our system provides the utmost flexibility in configuration and reporting by seamlessly integrating with almost any program or software you’re already using, so a perfect fit comes standard for every customer. Plus, you can be up and running in about a month with a solution that is fully customized to your organization’s needs.
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  • 4
    QuickBooks Online
    QuickBooks Online is the most popular accounting software in the world. QuickBooks Online makes accounting easy. Make tracking receipts, income, bank transactions, and more feel simple with the #1 small business accounting software. Snap photos of your receipts and link them to expenses right from your phone. Our agents are ready and available to answer all your QuickBooks questions. Use the apps you know and love to keep your business running smoothly. QuickBooks Online works on your PC, Mac, tablets, and phones. Click the link above to get a 30 day free trial and 50% off your first 3 months. More than accounting software. QuickBooks helps you track income, expenses, and stay ready for taxes. Customers find on average $3,534 in tax savings per year. Need more help? QuickBooks Live helps you stay organized and be ready for tax time. QuickBooks comes with a mobile app that help you run your business on the go—anytime, anywhere.
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    Starting Price: $9/month (normally $15/month)
  • 5
    Bright Funds

    Bright Funds

    Bright Funds

    Our personalized, intuitive platform is built for today’s employees, creating a more engaging user experience that inspires adoption. Consider us an extension of your team, from deployment to ongoing initiatives and product updates. We go beyond standard reporting tools, offering you expertise and strategic collaboration through our Client Experience services. Through our curated funds, impact updates, and more, we’re redefining how people connect with the causes that matter to them. Our intuitive skills-based volunteerism tool uncovers relevant opportunities, offering personalized recommendations that help employees give their time and talents. Employees can see how their donation is making a difference. Our team delivers updates from nonprofits to give people insight into their positive impact on the world.
    Starting Price: $2 per employee per month
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    Percent Pledge

    Percent Pledge

    Percent Pledge

    Percent Pledge creates tailored social impact programs, empowering companies and their employees to donate to and volunteer for the trusted charities they care about most. Give with ease, and improve employee engagement and employee retention with a customized workplace giving program. Facilitate philanthropy and measure company-wide impact on one, secure platform. Easy to manage for you, easy to use for your employees. Employees want to volunteer, and data shows that volunteer programs have a huge positive impact on morale and retention. Our volunteering platform and white glove services make your volunteer program more accessible to employees and create a higher-impact program requiring less effort from your team. Measure and market your impact per employee and company-wide. In addition to real-time dashboards, our personalized impact reporting delivers you data and authentic storytelling to fuel employee engagement and cause marketing.
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