*Note that some of these HR tools are available either as a paid add-on or included in premium plans. QuickBooks Payroll vs Paychex Side-by-Side Comparison Rippling: Best payroll software for companies employing remote or global workers or wanting a modular solution.Plus, sign up before December 1, 2023, and get your first month FREE! When neither Paychex Flex nor QuickBooks Payroll work for you, we found that Rippling is the best alternative, as it lets you mix and match HR, IT, and payroll modules. QuickBooks Payroll: Best for small businesses, especially those using QuickBooks accounting software.Paychex Flex: Best for growing startups with plans to scale.In this guide, we’ll take a look at both systems’ essential features, but if you’re looking to find the right payroll solution for your needs quickly, here are our recommendations: QuickBooks Payroll allows unlimited pay runs and integrates with Intuit products like QuickBooks (a popular small business accounting software), while Paychex Flex has scalable payroll solutions (from a one-person plan option to enterprise or PEO), more robust benefits options, and a higher level of HR support that’s great for businesses planning to grow significantly. Paychex Flex and QuickBooks Payroll are cloud-based payroll systems designed to help you process employee and contractor payments.
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