Launching and growing a startup is messy enough—payroll shouldn’t be. The best payroll platforms automate tax filings, handle multi-state rules, pay contractors and employees on time, integrate with your accounting stack, and scale from a handful of people to a distributed team without creating admin drag.
Below is a startup-friendly shortlist you can actually use, plus quick guidance on choosing the right fit for your stage and hiring model.
1. Gusto
Gusto is a go-to payroll solution for early-stage startups thanks to its clean interface and built-in automation. It handles everything from onboarding and tax filings to year-end forms. Startups can start with contractor-only payroll and later upgrade to support full-time employees. The software also includes employee self-service, benefits administration, and integrations with popular accounting systems, making it one of the most scalable options for small but growing teams.
2. Rippling
Rippling combines payroll with a wider HR and IT management platform, which is a big plus for startups that want all back-office functions under one roof. It automatically syncs employee data across payroll, benefits, and devices, reducing duplicate work. With advanced automation and workflow customization, Rippling suits startups that anticipate fast growth and want to minimize manual admin as they scale across states or even globally.
3. QuickBooks Payroll
For startups already using QuickBooks for accounting, QuickBooks Payroll integrates seamlessly. It offers automatic tax calculations, same-day direct deposit, and HR compliance tools. Its straightforward interface makes it easy for small teams without a dedicated finance professional to process payroll while keeping the books in sync. QuickBooks Payroll is especially attractive to finance-lean startups that want a familiar and consolidated system.
4. OnPay
OnPay is built with small businesses and startups in mind. It simplifies multi-state payroll, automatically handles tax filings, and provides strong support for both W-2 employees and 1099 contractors. The platform also includes HR tools like onboarding workflows, compliance checklists, and employee self-service. Its affordability and ease of use make it a smart choice for startups that want reliable payroll without heavy overhead costs.
5. ADP Run
ADP is a household name in payroll, and its “Run” product is tailored for startups and small businesses. It brings enterprise-level expertise in tax compliance and benefits administration to smaller teams. ADP Run supports everything from automated payroll runs to employee access portals. Startups benefit from its reliability, especially when dealing with multiple states and complex payroll requirements.
6. Paychex Flex
Paychex Flex offers a scalable payroll platform that adapts as a startup grows. It includes features like real-time payroll processing, compliance management, and benefits integration. Paychex is particularly strong in customer support, giving startups confidence that they won’t be left figuring things out alone. For teams that plan to expand steadily, Paychex Flex offers a flexible, future-proof option.
7. Deel
Deel is purpose-built for startups that hire globally. It simplifies international payroll, contractor payments, and compliance with local labor laws in over 100 countries. Deel handles contractor agreements, cross-border payments, and employer-of-record services, making it a lifesaver for remote-first startups. If your team spans multiple countries, Deel ensures payroll and compliance are no longer a headache.
8. Justworks
Justworks is a professional employer organization (PEO) that combines payroll, HR, compliance, and benefits in one platform. Startups benefit from its ability to offer enterprise-grade benefits and handle regulatory complexity without building an internal HR team. Justworks takes over much of the administrative burden, allowing founders to focus on growth while ensuring their people are paid and supported correctly.
9. Zenefits Payroll
Zenefits is an HR-first platform with payroll as part of its suite. For startups looking to bundle HR, benefits, and payroll, Zenefits streamlines everything into a single dashboard. It automates tax filings, provides employee self-service options, and integrates well with time tracking and scheduling. Zenefits is best for startups that want HR and payroll tightly linked, reducing the friction of using separate tools.
10. Square Payroll
Square Payroll is ideal for startups in retail, food, or service industries. It integrates with Square POS, making it easy to manage hourly workers, contractors, and employees. Square Payroll automatically calculates and files payroll taxes, provides direct deposit, and offers a simple interface for both managers and workers. For startups with hourly teams, its integration with scheduling and POS is especially powerful.
How to Choose (Fast) as a Startup?
Think in terms of “what do we need this quarter and next,” not a five-year overhaul. Prioritize:
- Automation & compliance: Automatic tax calculations/filings, new-hire reporting, and end-of-year forms.
- Contractor support: Smooth onboarding, global payouts (if needed), and 1099 handling.
- Integrations: Tight links to your accounting (e.g., QuickBooks), time tracking, and HR stack.
- Scalability: Multi-state, roles and permissions, custom earnings/deductions, and straightforward pricing.
- Global capability (if remote-first): EOR or in-country payroll when you hire outside your home country.
- Employee experience: Self-serve portals, clear pay stubs, quick updates, mobile-friendly.
Final Thoughts
The best payroll software for startups balances ease of use, automation, and scalability. If you’re a small U.S.-based team, Gusto or OnPay might fit perfectly. If you expect rapid scaling, Rippling or Paychex Flex can grow with you. For global hiring, Deel is unmatched. And if you want a full-service solution, Justworks as a PEO can be the partner you need.
The right payroll system not only saves hours of manual work but also builds trust with your team by ensuring accuracy and timeliness—two things every startup needs to thrive.
FAQs
1. What is the best payroll software for a startup with only contractors?
Contractor-only startups often benefit from software like Gusto (contractor plan) or Square Payroll, which streamline 1099 payments and tax forms without requiring a full payroll subscription.
2. How much does payroll software cost for startups?
Pricing varies widely. Entry-level plans for contractor-only payroll can start as low as $6 per contractor monthly, while more comprehensive plans with benefits and HR features typically range from $30 to $60 per month plus per-employee fees.
3. Can payroll software handle multiple states for compliance?
Yes. Options like OnPay, ADP Run, and Rippling specialize in multi-state compliance, automatically calculating state-specific taxes and handling reporting requirements.
4. Do startups need payroll software if they have only a few employees?
Even with just a handful of employees, payroll software reduces errors, ensures compliance, and saves hours of manual work. It’s often more cost-effective than doing payroll manually or outsourcing early on.
5. What is the best payroll software for startups hiring globally?
Deel and Rippling stand out for global payroll. They manage contractor payments across borders, currency conversions, and compliance with local employment laws.
6. Can payroll software integrate with accounting tools like QuickBooks or Xero?
Most modern payroll solutions integrate with accounting platforms. QuickBooks Payroll integrates directly with QuickBooks, while Gusto, OnPay, and Rippling connect seamlessly with QuickBooks, Xero, and other accounting systems.
7. What features should a startup prioritize in payroll software?
The key features include automated tax filing, contractor and employee support, compliance management, scalability for multi-state or global teams, and integrations with HR or accounting systems.
8. How long does it take to set up payroll software for a new startup?
Many platforms can be set up within a day, provided you have employee information, tax IDs, and bank details ready. Some solutions like Gusto and Square Payroll guide you step-by-step for faster onboarding.
