The 10 Best Payroll Software Tools For Startups

Choosing A Payroll Software Tool For Your Startup

Running a startup usually involves building your product, shaping your brand, supporting your team, and trying to keep up with everything. Among all this, managing payroll can be time-consuming and stressful. Even small mistakes can cause compliance issues, unhappy employees, or extra work. This is why picking the right payroll software for startups is one of the smartest decisions you can make. A good payroll solution does exactly that: it helps you automate repetitive tasks, stay compliant with local laws, manage employee information, and ensure everyone is paid accurately and on time. It also reassures you, knowing that all the payroll processes are managed while you focus on growing your business.

With so many tools available, it can be overwhelming to know where to start. The key is to choose software that fits your current business needs but can also adapt as your team grows. Factors like ease of use, pricing, customer support, integrations, and compliance features are all important in making the best choice. In this article, we explore the 10 best payroll software tools for startups to help you understand what each option offers and choose the one that fits your needs.

Table Of Contents

The Benefits Of Using A Payroll Service For Your Startup

• Saves you valuable time so you can focus on growing your business.
• Reduces errors by automating calculations, taxes, and payments.
• Helps you stay compliant with changing laws and regulations.
• Ensures employees get paid accurately and on time.
• Offers easy access to reports for budgeting and planning.
• Simplifies tax filing and end-of-year paperwork.
• Boosts security by keeping sensitive payroll data protected.
• Scales with your startup as your team grows.
• Gives you peace of mind knowing experts handle the complex stuff.

The 10 Best Payroll Providers For Startups

1. Gusto

Best For

Small to mid-sized US startups seeking an easy and friendly payroll and HR solution.

Pros

• Super user-friendly setup.
• Full-service payroll (tax filings included).
• Good benefits integrations.
• Strong onboarding tools.
• Good support for contractors and employees.

Cons

• The cost can increase as you add employees or advanced HR features.
• Some advanced features are reserved for higher tiers.

Notable Features

• Unlimited pay runs.
• Automated federal/state tax filing.
• Employee self-service.
• Benefits (health, 401(k)) integration.
• Time tracking add-ons.
• Starter templates for startups.

Pricing

• Simple Plan: $49 per month, plus $6 per month per person.
• Plus Plan: $80 per month, plus $12 per month per person.
• Premium Plan: $180 per month, plus $22 per month per person.

Check Gusto’s plans for the latest offers and any startup promotions.

2. Rippling

Best For

Startups that want payroll integrated with IT, HRIS, device, and app management.

Pros

• Extremely modular (HR, benefits, device management).
• Strong automation across HR, payroll, and IT.
• Scalable.

Cons

• More complex and expensive than niche payroll tools.
• Pricing is often custom, so you’ll need a quote.
• Steeper learning curve if you only want basic payroll.

Notable Features

• Unified employee data across payroll, benefits, and apps.
• Automated onboarding and offboarding.
• Global payroll and contractor features.
• Lots of integrations.

Pricing

Typically, custom quotes are provided. However, Rippling offers modular pricing and a platform approach, so please contact their sales team for startup pricing.

3. RUN Powered By ADP

Best For

Startups seeking a provider with reliable tax compliance and optional HR support.

Pros

• Payroll and tax expertise.
• Lots of package options for very small businesses up to mid-size.
• Strong compliance support.
• Payroll tax filing.

Cons

• The interface and pricing can feel more corporate.
• There is lower transparency in online pricing for some packages.
• This may be overkill for very small teams that want simple tools.

Notable Features

• Tiered packages (basic payroll to full HR bundles).
• Payroll tax filing.
• Veteran support.
• Integrations (time, benefits, accounting).

Pricing

ADP offers small-business packages at different levels. While some starting prices for small payroll packages are publicly available, many plans require you to request a quote. ADP often shows a low starting price in its marketing materials, but these numbers are just examples.

4. Paychex

Best For

Startups that need payroll services, along with support for benefits and retirement plans.

Pros

• Full payroll processing.
• Tax administration.
• Benefits and retirement integrations.
• Scalable.
• Strong customer service.

Cons

• Pricing is often customized and can be more expensive than competitor brands.
• Some small startups may find that the offering includes more than they really need.

Notable Features

• Automated payroll and tax filing.
• Integrated benefits and 401(k) options.
• Workforce management tools.
• Compliance resources.

Pricing

Paychex usually provides custom quotes. You might see basic numbers like “starting around $39/month plus a fee for each employee” for entry-level packages in public reviews. However, it’s better to get a personalized quote.

5. QuickBooks Payroll

Best For

Startups that already use QuickBooks accounting and want easy bookkeeping and payroll integration.

Pros

• Smooth QuickBooks integration.
• Automated tax filing.
• Multiple payroll tiers (Core/Premium/Elite) to suit growing teams.
• Familiarity for accountants.

Cons

• If you’re not using QuickBooks, you won’t benefit from the same features.
• Some advanced payroll and HR functions are available only in higher plans.

Notable Features

• Direct integration with QuickBooks Online.
• Automatic tax deposits and filings.
• Next-day direct deposit options on certain plans.
• Additional HR and support add-ons.

Pricing

• Payroll Core and Simple Start: $26.40 per month, plus $6.50 per employee each month.
• Payroll Core and Essentials: $37.50 per month, plus $6.50 per employee each month.
• Payroll Premium and Plus: $60.90 per month, plus $10 per employee each month.

Check QuickBooks’ payroll pricing page for specific costs and current promotions, as these prices may change.

6. Square Payroll

Best For

Small retail, cafe, or restaurant startups that already use Square for payments, or businesses with employees who receive tips.

Pros

• Simple pricing.
• Great for teams with both traditional employees (W-2) and independent contractors (1099).
• Built-in tip tracking and timecard features that work with Square POS.
• Affordable option for contractor-only payroll.

Cons

• It doesn’t have as many features as larger HR platforms.
• It’s not the best choice if you need complex HR processes or international payroll.

Notable Features

• There is a contractor-only plan.
• Payroll for both employees and contractors.
• Tip tracking.
• Integration with Square POS and Square Team.
• Direct deposit.
• Tax filing for teams in the US.

Pricing

• Full-Service Payroll: $35 per month, plus $6 for each person paid.
• Contractor-Only Payroll: $6 per month per person.

Check Square’s official pricing page for the most up-to-date information.

7. OnPay

Best For

Startups looking for clear and affordable pricing with basic payroll and HR features.

Pros

• Easy-to-understand pricing.
• Unlimited payroll runs.
• Included payroll tax filings.
• Strong customer support.
• Simple setup.
• Friendly for small teams.

Cons

• Fewer advanced HR features for larger companies compared to full HCM platforms.

Notable Features

• Unlimited payroll runs.
• Handling of W-2/1099 forms.
• Year-end filings.
• Support for multi-state payroll.
• Straightforward help for onboarding and migration.

Pricing

There is only one plan, with a $49 monthly base fee and an additional $6 per month per person. Refer to OnPay’s pricing page for the latest details.

8. Deel

Best For

Startups that hire global contractors and international employees and need compliant payroll and Employer-of-Record (EOR) services for cross-border operations.

Pros

• Strong international payroll.
• Easy payments for contractors.
• Options to hire without needing local entities.
• Multi-currency payouts.
• Support for local compliance.

Cons

• Using international services and EOR options can increase costs.
• Pricing varies depending on the country and service type.
• Deel is not just a simple tool for local payroll.

Notable Features

• Global contractor payroll.
• EOR services that take on local employer responsibilities.
• Contractor management.
• Resources for localized contracts and compliance.

Pricing

• Deel EOR: $599 per employee per month.
• Deel Contractor Management: $49 per contractor per month.
• Deel Contractor of Record: $325 per contractor per month.
• Deel PEO: $95 per employee per month.
• Deel US Payroll: Custom quote.
• Deel Global Payroll: $29 per employee per month.

Check Deel’s pricing pages for specific details by country.

9. Remote

Best For

Startups that hire internationally and need global payroll or EOR services with clear pricing.

Pros

• Clear options for contractor payroll.
• Full global payroll and EOR.
• Manages local taxes and benefits.
• Helpful for startups growing across borders.

Cons

• EOR and full global employment can be costly for very small teams.
• Extra features and specific country details may increase total costs.

Notable Features

• Contractor management.
• Global payroll.
• EOR services.
• HRIS and integrations.
• Local compliance handling.

Pricing

• Employer of Record: $699 per employee per month.
• Payroll: $29 per employee per month.
• Contractor Management: $29 per contractor per month.
• Contractor Management Plus: $99 per contractor per month.
• Contractor of Record: From $325 per contractor per month.
• Professional Employer Organization: From $99 per employee per month.
• Equity: From $39 per year.

For startups, there’s tailored pricing, so please check Remote’s pricing page.

10. Zenefits

Best For

Startups looking for an HR platform that includes payroll as an optional feature. This is a good choice if you want HR, benefits, and payroll in one place.

Pros

• Competitive pricing for each employee using the HR platform.
• Integrated benefits management.
• Time and attendance tracking.
• Optional payroll add-ons.

Cons

• Payroll is an add-on to the base HR plan, so the total cost depends on which modules you select.
• Some startups might prefer a dedicated payroll service instead of an all-in-one HR solution.

Notable Features

• Onboarding.
• Time off management.
• Employee records.
• Tools for benefits and ACA compliance.
• Optional payroll and tax filing modules.
• Various plan tiers.

Pricing

Zenefits usually provides per-employee monthly pricing for HR plans, with payroll and benefits as additional options. Visit Zenefits’ site or ask for a demo to get exact pricing and minimum requirements for each module.

Quick Tips

• If you use QuickBooks for accounting, QuickBooks Payroll can make bookkeeping easier.
• If you plan to hire people internationally, choose Deel, Remote, or Rippling for global payroll and EOR support.
• For simple and low-cost contractor payroll, Square and similar services can be a good option.
• If you want a user-friendly startup experience with strong benefit options, Gusto and OnPay are often recommended.

Conclusion

Choosing the right payroll provider can make a huge difference in how smoothly your startup runs. Each option comes with its own strengths, whether you want something simple and budget-friendly or a full platform that scales as you grow. The key is knowing what your team needs today and what you’ll need in a few months’ time. To simplify the decision-making process, visit our payroll software directory and filter solutions according to your specific needs. No matter which provider you choose, having reliable payroll helps your startup succeed.