Best Accounting Software for Paychex Flex

Find and compare the best Accounting software for Paychex Flex in 2026

Use the comparison tool below to compare the top Accounting software for Paychex Flex on the market. You can filter results by user reviews, pricing, features, platform, region, support options, integrations, and more.

  • 1
    Sage Intacct Reviews
    Top Pick
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    Sage Intacct is an all-encompassing cloud accounting platform tailored to meet the dynamic demands of expanding businesses. It features powerful tools for managing the general ledger, accounts payable, accounts receivable, and multi-entity operations. With real-time reporting and interactive dashboards, users can gain valuable insights into crucial financial indicators, facilitating informed decision-making. The software accommodates various currencies and locations, making it suitable for international business activities. Its built-in automation streamlines data entry, reduces the likelihood of mistakes, and speeds up the month-end closing process. Additionally, Sage Intacct easily integrates with other business systems such as payroll, customer relationship management, and inventory, improving overall operational efficiency. The platform's customizable workflows and permission settings ensure strong internal controls and audit preparedness. Finance teams rely on Sage Intacct for its scalability, dependability, and adherence to compliance standards.
  • 2
    Xero Reviews
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    Xero

    Xero

    $20/month
    5,414 Ratings
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    Xero is a robust cloud-based accounting solution designed specifically for small enterprises. With Xero, users can efficiently handle their cash flow, monitor expenditures, process online payments, and access a wide range of additional features—all within the Xero platform.
  • 3
    QuickBooks Online Reviews
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    QuickBooks Online

    Intuit

    $9/month (normally $15/month)
    45 Ratings
    QuickBooks Online is the most widely used accounting software in the entire world. QuickBooks Online simplifies accounting. Accounting software for small businesses that is #1 makes it easy to track receipts, income, transactions and more. You can take photos of receipts to link them with expenses. Our agents are available to answer any questions you may have about QuickBooks. Keep your business running smoothly by using the apps that you love. QuickBooks Online is compatible with PCs, Macs, tablets and phones. Click the link to get a 30-day free trial, and 50% off for your first three months. QuickBooks is more than just accounting software. QuickBooks helps you keep track of your income and expenses so that you can prepare for taxes. Customers save an average of $3,534 per year. Need more help? QuickBooks Live helps you to stay organized and ready for tax season. QuickBooks Mobile is a mobile application that helps you run your business anywhere, anytime.
  • 4
    Bookkeeper360 Reviews

    Bookkeeper360

    Bookkeeper360

    $19 per month
    Customized accounting, technology, and advisory solutions designed specifically for you can greatly reduce the frustrations and unexpected financial issues that arise from disorganized records and inaccurate bookkeeping. We are committed to delivering precise and timely financial insights that reflect the state of your business. Remember, your passion lies in building your business, not managing an accounting team. Our dedicated group of CPAs, advisors, and tech specialists are fully equipped to support your success with the right resources. Our entirely US-based workforce employs innovative technology to handle your accounting needs while maintaining a personal connection. Bookkeeper360 is a trusted partner for thousands of small businesses across the country and has earned accolades as a two-time recipient of Xero’s Top Partner of the Year award, in addition to being named one of Inc. 5000’s Fastest-Growing Companies for the last three consecutive years. Recognized as an industry leader, Bookkeeper360 has also been featured in prestigious publications such as Forbes, Accounting Today, Business Insider, and CPA Practice Advisor, showcasing our commitment to excellence and innovation. Our mission is to provide you with peace of mind, allowing you to focus on the growth of your business while we take care of the numbers.
  • 5
    Neo.Tax Reviews

    Neo.Tax

    Neo.Tax

    2% ttl qualifying R&D expenses
    Neo.Tax has automated preparing the R&D Tax Credit for startups and accountants. We have simplified the complex process of applying for Federal and State R&D Tax Credits. Startups can get up to $250k back in under an hour. Our flexible app allows you to prepare your R&D tax credit on your own, be guided by our team, or anything in between. Whichever route you choose, all claims are reviewed by our tax experts so you can file your credit with complete confidence. The R&D Tax Credit is best for startups and small businesses investing in R&D who made less than $5M to no revenue, have been profitable less than 5 years, and had R&D work done by US based employees or contractors. This is the first step towards turning taxes into a modern advantage for accountants and businesses. Neo.Tax is building the easiest and most accurate tax and accounting automation software.
  • 6
    QuickBooks Online Advanced Reviews
    Equip your business with essential tools to enhance efficiency and gain valuable insights for growth, all available through QuickBooks Online Advanced. Access the critical data you require with reports that are not only customizable but also ready for presentation, while ensuring that your spreadsheets are synchronized for precise business information and tailored insights. Reduce the burden of manual tasks by effortlessly importing and dispatching numerous invoices and expenses simultaneously, and streamline the process of entering and modifying multiple bills and checks within a few simple steps. We prioritize your security by safeguarding your financial details with advanced encryption and robust protective measures. Personalize your workflow by selecting from a range of seamless app integrations specifically designed for QuickBooks Online Advanced, and enhance its capabilities by connecting with top-tier applications like DocuSign, Bill.com, HubSpot, and Salesforce, among others. With these features, you can significantly improve your business operations and drive success more effectively.
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