Running a startup often means wearing multiple hats, from product development and marketing to hiring and payroll. Managing payroll efficiently is crucial—not only to stay compliant with tax regulations but also to build trust and retain employees. However, startups face unique challenges such as tight budgets, lean teams, and the need for scalable systems. That’s where modern payroll software comes in.

The right payroll solution can automate routine tasks, ensure timely and accurate payments, and integrate seamlessly with other business tools. In this article, we’ll explore the 10 best payroll software options tailored for startups—covering features, ease of use, scalability, and affordability.

1. Gusto

Gusto is one of the most popular payroll solutions for startups, and for good reason. It combines payroll, HR, and benefits administration into a single, easy-to-use platform. Startups can run payroll in just a few clicks, automate tax filings, and even offer employee benefits such as health insurance and retirement plans.

What sets Gusto apart is its clean interface and employee self-service features. Team members can log in to access pay stubs, update personal information, and view benefits without HR intervention. Gusto also supports contractor payments, time tracking, and offers integrations with accounting tools like QuickBooks and Xero—making it ideal for startups that want an all-in-one, scalable solution.

2. OnPay

OnPay offers a straightforward and transparent approach to payroll that startups appreciate. Its simple pricing model includes all core features without add-on fees or confusing tiers. The platform supports both salaried and hourly workers, automates tax filings across multiple states, and handles new hire reporting.

What makes OnPay especially appealing for early-stage companies is its ability to integrate seamlessly with accounting software like QuickBooks Online and Xero. It also includes basic HR features such as employee onboarding, document storage, and benefits administration — making it more than just a payroll processor. The clean interface and responsive support team help founders get set up quickly, which is invaluable when you’re wearing multiple hats. For budget-conscious startups that still want full-service payroll, OnPay delivers strong value without sacrificing functionality.

3. QuickBooks Payroll

For startups already using QuickBooks for accounting, QuickBooks Payroll is a natural extension. It allows founders and finance leads to keep payroll and bookkeeping tightly integrated. You can run payroll with same-day direct deposit, automatically calculate and file taxes, and sync all payroll expenses directly into your QuickBooks ledger.

QuickBooks Payroll offers a range of plans to suit growing businesses. As your startup adds more employees or contractors, the system can handle more complex needs like multiple pay schedules, benefits integration, and even HR support. The biggest advantage is the real-time sync between payroll and accounting, reducing the chance of discrepancies. For startups that prioritize financial accuracy and want to avoid double-entry headaches, QuickBooks Payroll is a logical and reliable choice.

4. Remote

Remote is a simple, secure platform to find, hire, manage, and pay talent anywhere, seamlessly and compliantly. Remote is the all-in-one HR and payroll platform to find, hire, manage, and pay your entire team everywhere. Whether onboarding your first cross-border hire or scaling across continents, Remote delivers enterprise-grade compliance, intuitive design, and dedicated local expertise. With one platform for every contract, payslip, and regulation, Remote helps you grow without borders.

5. ADP

ADP RUN is part of ADP’s extensive suite of payroll and HR services, tailored specifically for small and growing businesses. It provides robust payroll processing, automated tax filing, compliance support, and access to benefits and retirement plans. One of its key strengths is its scalability — as your team expands, ADP can accommodate more complex needs like time tracking, advanced HR, and even global payroll.

Startups that are preparing for rapid growth or hiring in multiple states will appreciate ADP’s focus on compliance. The platform helps you navigate labor laws, tax regulations, and reporting requirements, which can be overwhelming for first-time founders. It also offers add-ons like background checks and onboarding tools. While it may come with a higher price tag compared to some simpler platforms, ADP RUN offers enterprise-grade reliability and infrastructure — ideal for startups that plan to grow fast.

6. Square Payroll

Square Payroll is a standout solution for startups in retail, hospitality, and other industries with hourly or part-time staff. Built by Square (the popular point-of-sale provider), it integrates directly with Square’s time-tracking tools, making it easy to calculate wages based on actual hours worked. This is especially useful for startups with fluctuating schedules or seasonal staff.

Square Payroll handles tax filings, direct deposit, and employee self-service portals. It also supports paying contractors, which is a big plus for early-stage companies working with freelancers. The platform offers flexible pricing — you only pay when you run payroll, making it great for businesses with variable staffing needs. If your startup already uses Square for payments or POS, adding Square Payroll can streamline operations significantly.

7. Rippling

Rippling is more than just payroll software — it’s a comprehensive employee management platform that automates HR, IT, and finance processes all in one place. For startups that want to centralize onboarding, payroll, benefits, device management, and app provisioning, Rippling offers unmatched automation and integration.

Payroll with Rippling is lightning-fast — you can run payroll in 90 seconds with automatic tax filings in all 50 states. But what really sets it apart is how it connects payroll to the rest of your business systems. New hires are automatically added to payroll, given access to company apps, and even shipped laptops — all triggered from a single onboarding flow. For tech-savvy startups or those planning to scale quickly, Rippling’s automation and modular design make it an incredibly powerful tool.

8. Patriot Payroll

Patriot Payroll is a budget-friendly software that offers both self-service and full-service payroll options. The self-service plan is great for founders who want to stay hands-on and file taxes themselves, while the full-service plan handles tax filings for you. Both versions include direct deposit, customizable pay schedules, and easy reporting.

What makes Patriot appealing to startups is its simplicity. The setup is quick, the pricing is transparent, and the support is responsive. While it doesn’t offer as many HR bells and whistles as platforms like Gusto or Rippling, it delivers reliable payroll processing at a fraction of the cost. For early-stage startups that just want to get payroll right without overpaying, Patriot Payroll offers excellent value.

9. Deel

Deel is built for startups with a global or remote workforce. It enables companies to hire, pay, and manage employees and contractors in over 150 countries while staying compliant with local labor laws. Deel acts as the employer of record (EOR), allowing you to legally hire in countries where your startup doesn’t have a legal entity.

For startups embracing remote-first or borderless teams, Deel simplifies the complexity of global payroll. It supports multi-currency payments, localized contracts, tax compliance, and even benefits for international hires. The platform also offers self-service onboarding and dashboards for both employers and employees. If your startup is hiring across borders or planning to expand globally, Deel is one of the most comprehensive and startup-friendly international payroll solutions available today.

10. Justworks

Justworks takes a unique approach by offering payroll through a PEO (Professional Employer Organization) model. This means your startup enters a co-employment relationship with Justworks, allowing you to offer enterprise-level benefits like health insurance, 401(k), and wellness programs without negotiating with providers directly.

The platform handles payroll, tax filings, compliance, and HR support. It’s ideal for startups that want to compete for top talent by offering strong benefits but don’t have the time or resources to manage everything in-house. Justworks also provides dedicated support, helping founders stay compliant with labor laws and best practices. For fast-growing startups that want a “done-for-you” solution covering payroll, HR, and benefits, Justworks is a top contender.

Key Factors to Consider When Choosing Payroll Software

Selecting the best payroll software for your startup depends on several factors:

• Team Size – Some platforms are better suited for micro-teams or solo founders, while others scale to support dozens or hundreds of employees.
• Budget – Look for transparent pricing that aligns with your current stage and anticipated growth.
• Compliance Needs – Multi-state or international operations require tools with robust tax and legal compliance support.
• Integration – Ensure the software works with your existing accounting, time-tracking, and HR tools.
• Ease of Use – Startups benefit from intuitive interfaces and employee self-service features to reduce administrative workload.

Final Thoughts

Choosing the best payroll software for your startup depends on your current needs, your growth trajectory, and your team structure. A lean team working in one state might prioritize affordability and simplicity, while a fast-scaling startup hiring globally will need compliance tools, automation, and flexibility.

Here’s a quick summary to guide your decision:

• Best for all-in-one HR + payroll: Gusto, Rippling
  
• Best for QuickBooks users: QuickBooks Payroll
  
• Best for global hiring: Deel
  
• Best for hourly or seasonal teams: Square Payroll
  
• Best for cost-conscious startups: OnPay, Patriot Payroll
  
• Best for growing with compliance needs: ADP RUN, Justworks
  
• Best for simplicity and speed: SurePayroll
  

At the end of the day, your payroll software should reduce your administrative load, not add to it. Look for a platform that fits your team size, integrates with your existing tools, and can grow with your business. Investing in the right payroll system early on sets a strong foundation — allowing you to focus more on building your product, your team, and your vision.