You’ve made your first few hires. The excitement of growing your team quickly fades when you realize someone has to actually pay these people, on time, with the right taxes withheld, in compliance with whatever state they happen to live in.
Welcome to payroll. It’s not glamorous, but getting it wrong is expensive. Late payments tank morale. Tax mistakes trigger IRS penalties. And as a founder, you have better things to do than manually calculate withholdings every two weeks.
The good news: modern payroll software for startups handles almost everything automatically. The bad news: there are dozens of options, and choosing the wrong one means switching later, a painful process that involves re-entering employee data, reconfiguring tax settings, and hoping nothing breaks during the transition.
Here’s a breakdown of the best payroll solutions for startups with under 50 employees, what makes each one stand out, and which type of company each serves best.
7 Best Payroll Software Options for Startups in 2026
1. Gusto: Best All-Around for Most Startups
Gusto has become the default choice for early-stage startups, and for good reason. Used by over 400,000 companies, it combines payroll, benefits administration, and basic HR tools in one clean interface that doesn’t require an accounting degree to navigate.
The platform shines in its simplicity. Running payroll takes just a few clicks, and Gusto handles all federal, state, and local tax filings automatically—with a guarantee to cover any penalties if they make a mistake. For startups hiring their first employees, that peace of mind is worth its weight in gold.
What makes it stand out:
- Automatic tax filings in all 50 states with error-free guarantee
- Built-in health insurance, 401(k), and workers’ comp administration
- Employee self-service portal for pay stubs, tax documents, and benefits enrollment
- Integrates with 180+ tools including QuickBooks, Xero, and most accounting software
- Equity compensation support with cap-table-friendly reports (critical for funded startups)
- No contracts—pay month-to-month and cancel anytime
Pricing:
- Simple Plan: $49/month + $6/employee — single-state payroll, basic HR
- Plus Plan: $60/month + $9/employee — multi-state payroll, time tracking, advanced onboarding
- Premium Plan: $135/month + $16.50/employee — dedicated support, compliance alerts, HR resource center
Best for: Startups hiring W-2 employees across multiple states who want payroll and benefits in one system. If you’re between 5-50 employees without a dedicated HR person, Gusto handles the complexity without overwhelming you. It’s particularly strong for pre-seed to Series A startups looking for a scalable, affordable payroll hub.
2. Rippling: Best for Tech-Forward Teams
Rippling goes beyond payroll into full workforce management. It connects payroll to IT (device management, app provisioning) and HR (onboarding, offboarding) in ways competitors simply can’t match.
The platform’s superpower is automation. When you hire someone, Rippling can set up their payroll, enroll them in benefits, provision their laptop, create their email account, and grant access to Slack—all from a single workflow. When someone leaves, one click revokes everything. For fast-growing startups juggling multiple systems, this level of integration eliminates hours of manual work.
Rippling automates 95% of payroll admin and processes pay runs in minutes with a single click. The platform also offers global payroll across 90+ countries, making it a strong choice for distributed teams.
What makes it stand out:
- Onboard a new hire in 90 seconds—payroll, benefits, laptop, and app access configured automatically
- Built-in device management (ship laptops globally, wipe them remotely when someone leaves)
- Global payroll for international employees and contractors in 90+ countries
- 600+ software integrations with accounting, HR, and business tools
- Highly customizable no-code workflow automations
- Unified platform connecting HR, IT, and Finance data
Pricing:
- Base HRIS module starts at $8/employee/month + $35/month base fee
- Full platform (HRIS, Payroll, Benefits, Time) typically runs $15-25/employee/month
- Complex setups with global payroll and IT management: $30-50+/employee/month
- EOR services: $499-599/employee/month
Best for: Tech startups with remote teams, especially those hiring internationally or managing company devices. The learning curve is steeper than Gusto, but the automation payoff is significant if you’re scaling quickly. Rippling is ideal for companies that want one platform to rule HR, IT, and payroll.
3. Deel: Best for International & Contractor-Heavy Teams
If your team spans multiple countries or relies heavily on contractors, Deel solves problems other platforms can’t touch. It handles compliant payments in 150+ countries without requiring you to set up local entities—a process that typically costs $20,000+ and takes months.
Deel has grown to serve over 35,000 companies worldwide, from small startups to publicly traded enterprises. The platform combines HRIS, payroll, compliance, benefits, and contractor management into one system built specifically for distributed teams.
What sets Deel apart is its depth of global expertise. The company employs in-house payroll specialists who understand local tax laws, employment regulations, and payment requirements in each country. When you hire someone in Germany, Brazil, or Singapore, Deel handles the compliance automatically.
What makes it stand out:
- Pay contractors and employees in 150+ countries compliantly
- Employer of Record (EOR) service lets you hire full-time employees abroad without establishing a local company
- Automated compliance with local labor laws, tax regulations, and employment standards
- Same-day payments in many regions with 120+ currency support
- Multiple withdrawal methods: ACH, SWIFT, Wise, Payoneer, Coinbase, and Deel prepaid cards
- Year-end tax form generation (1099s, W-2 equivalents) directly in platform
- AI-powered compliance monitoring and automated workflows
Pricing:
- Global Payroll: $29/employee/month (for your own entities)
- Contractor Management: $49/contractor/month
- Contractor of Record: $325/contractor/month
- PEO: $95/employee/month
- EOR (Employer of Record): $599/employee/month
Best for: Startups with distributed international teams or those hiring contractors globally. If you’re US-only with W-2 employees, Deel is overkill—but for global teams, it’s often the only realistic option that doesn’t require setting up foreign subsidiaries.
4. Justworks: Best PEO for Premium Benefits Access
Justworks operates as a Professional Employer Organization (PEO), which means they become the employer of record for tax and benefits purposes. This gives small startups access to enterprise-level benefits packages at group rates typically reserved for companies with 500+ employees.
The PEO model works particularly well for startups competing for talent against larger companies. When you can offer the same quality health insurance as Google at a fraction of the cost, recruiting becomes significantly easier. Justworks partners with major carriers like Aetna, UnitedHealthcare, and MetLife to provide comprehensive coverage options.
Justworks is a certified PEO (CPEO), meaning they meet strict IRS requirements for financial stability and compliance. They’re transparent about pricing—no hidden fees or surprise charges—and their platform consistently earns high marks for usability.
What makes it stand out:
- Access to enterprise-level health, dental, vision, and 401(k) plans at group rates
- Justworks handles all compliance, taxes, and HR administration as co-employer
- Dedicated support team with actual humans who answer the phone
- Simple flat-rate pricing with no hidden fees
- Cloud-based platform accessible from any device
- Supports remote and distributed teams across all US states
- Workers’ comp, commuter benefits, and HSA/FSA administration included
Pricing:
- Payroll Plan: $8/employee/month + $50/month base — standalone payroll only
- PEO Basic: $59/employee/month — payroll, compliance, core HR
- PEO Plus: $109/employee/month — everything in Basic plus health insurance, 401(k), HSA/FSA, mental health benefits
- Time Tracking Add-on: $8/employee/month
- International Contractors: $39/contractor/month
- EOR: $599/employee/month
Best for: Startups between 10-50 employees who want premium benefits to compete for talent but don’t want to manage HR internally. The PEO model works well until you hit ~100 employees, at which point bringing HR in-house often makes more financial sense. Ideal for US-based companies—the mobile app only works domestically.
5. OnPay: Best Budget-Friendly Option
OnPay delivers solid payroll functionality at a price point that won’t strain a bootstrapped budget. With over 30 years of payroll processing experience, the company has evolved from a traditional payroll service into a modern cloud platform while maintaining its focus on reliability and customer service.
The platform consistently earns top ratings—averaging 4.8 out of 5 stars across Capterra, G2, and TrustPilot. Where larger platforms nickel-and-dime you for features, OnPay includes everything in one straightforward price: unlimited payroll runs, all tax filings, HR tools, and integrations.
OnPay claims to save business owners over 15 hours per month compared to manual payroll processing. For a bootstrapped founder wearing multiple hats, that’s time you can redirect toward building your product or talking to customers.
What makes it stand out:
- Unlimited payroll runs at no extra charge (bonuses, corrections, off-cycle payments included)
- Error-free tax filing guarantee for all federal, state, and local taxes
- Includes basic HR features: onboarding, PTO tracking, document storage, compliance audits
- Dedicated account managers with responsive customer support
- Support for niche industries: restaurants (tip credits), farms (H-2A visas), nonprofits, construction
- Integrates with QuickBooks, Xero, When I Work, Deputy, and other popular tools
- One-month free trial to test before committing
Pricing:
- Single Plan: $49/month + $6/employee — includes everything (no tiers to navigate)
Best for: Early-stage startups watching every dollar who need reliable payroll without advanced HR or benefits management. If you’re pre-revenue, bootstrapping, or simply want payroll that just works without complexity, OnPay delivers exceptional value. It’s particularly strong for specific industries like restaurants, agriculture, and nonprofits that need specialized compliance support.
6. QuickBooks Payroll: Best for QuickBooks Users
If you’re already running your accounting on QuickBooks (and many startups are), their payroll add-on creates a seamless experience. Everything syncs automatically—payroll expenses flow directly into your books without manual reconciliation or CSV exports.
QuickBooks Payroll offers same-day direct deposit (on Premium and Elite plans), which is a meaningful perk when you’re building trust with new employees. The platform handles federal, state, and local tax calculations automatically and files everything on your behalf.
The integration advantage is real: when payroll data lives in the same system as your accounting, month-end closes become significantly easier. You eliminate the data entry errors and reconciliation headaches that plague companies using separate systems.
What makes it stand out:
- Native integration with QuickBooks accounting—zero reconciliation needed
- Same-day direct deposit available (Premium/Elite plans)
- Automatic tax calculations and filings for federal, state, and local taxes
- Employee self-service portals for pay stubs and tax forms
- Multi-state payroll support
- Automated payroll runs with scheduling for recurring payments
- Robust security with encryption and secure access protocols
Pricing:
- Core: $50/month + $6.50/employee — basic payroll, federal and state taxes
- Premium: $85/month + $9/employee — same-day deposit, HR support, time tracking
- Elite: $130/month + $11/employee — tax penalty protection, personal HR advisor
Best for: Startups already using QuickBooks Online for accounting who want everything in one system. If you’re using Xero or another accounting platform, the integration advantage disappears and other options become more competitive. Note that QuickBooks Desktop users should be aware of significant pricing increases coming in 2026.
7. Paychex Flex: Best for Compliance-Heavy Industries
Paychex serves over 740,000 businesses and brings enterprise-grade compliance capabilities to smaller companies. If you’re in an industry with complex regulatory requirements—healthcare, construction, restaurants, manufacturing—their depth of expertise matters.
The company employs more than 200 HR compliance experts who track regulatory changes across all 50 states, from tax updates and pay equity laws to workplace safety and privacy requirements. This isn’t just software; it’s software backed by human expertise that can help you navigate tricky situations.
Paychex Flex scales smoothly as you grow. The same platform that handles your 10-person team can manage 1,000+ employees, which means you won’t need to migrate to a new system when you hit growth milestones.
What makes it stand out:
- Dedicated HR advisor included in most plans
- 200+ compliance experts monitoring regulations across all 50 states
- Robust compliance support for regulated industries (healthcare, construction, restaurants)
- Time and attendance tracking built into the platform
- Nearly 300 third-party integrations
- AI-powered performance analytics and employee engagement surveys (2025 features)
- Support for W-2 employees, 1099 contractors, multiple pay schedules
- 24/7 customer support
Pricing:
- Essentials: $39/month + $5/employee — payroll, tax admin, basic workforce management
- Select: Custom pricing — adds HR tools, onboarding, background checks
- Pro: ~$47/month + $3/employee — state unemployment insurance, garnishments, GL services
- Enterprise: ~$95/month + $3/employee — performance management, document management, advanced analytics
Best for: Startups in regulated industries or those planning to scale quickly past 50 employees. The interface feels more “enterprise” than founder-friendly, and some users report inconsistent customer service, but the compliance depth and scalability are unmatched for companies with complex requirements.
How to Choose the Right Payroll Software
The “best” payroll software depends entirely on your specific situation. Here are the key questions to ask:
Where are your employees located?
- US-only, single state: Gusto, OnPay, or QuickBooks Payroll
- US-only, multiple states: Gusto Plus, Rippling, or Justworks
- US + international contractors: Deel or Rippling
- Full-time international employees: Deel EOR, Rippling EOR, or Justworks EOR
What’s your budget reality?
- Bootstrapped/pre-revenue: OnPay ($49 + $6/employee)
- Seed-funded, 5-20 employees: Gusto Simple ($49 + $6/employee)
- Series A+, scaling quickly: Rippling or Justworks
- Enterprise benefits on startup budget: Justworks PEO Plus ($109/employee)
Do you need benefits administration?
- Premium benefits to compete for talent: Justworks (PEO model gives group rates)
- Standard benefits, integrated: Gusto Plus or Premium
- Just payroll, handle benefits separately: OnPay or QuickBooks
What tools do you already use?
- QuickBooks accounting: QuickBooks Payroll (native integration)
- Xero accounting: OnPay or Gusto (both integrate well)
- Heavy IT management needs: Rippling (unified HR/IT platform)
- Nothing yet: Gusto (most integrations, easiest learning curve)
How complex is your compliance situation?
- Standard office/remote work: Any option works
- Regulated industry (healthcare, construction, etc.): Paychex Flex
- International hiring compliance: Deel
- Multiple pay types, unions, complex requirements: Paychex Flex or Rippling
Making the Switch
If you’re already using a payroll provider and considering switching, timing matters. The best windows for migration:
- Beginning of a quarter — cleaner tax filings, less reconciliation
- Beginning of a calendar year — fresh W-2 cycle, simplest transition
- After closing a funding round, budget for implementation costs and potential parallel runs
What to expect:
Most providers offer migration assistance, but expect the transition to take 2-4 weeks minimum. Run parallel payrolls during the first cycle to catch any discrepancies before cutting over completely.
Request a data export from your current provider, including:
- Employee information (names, addresses, SSNs, hire dates)
- YTD payroll data (wages, taxes withheld, deductions)
- Tax filing history
- Benefits enrollment information
Final Thoughts
Payroll isn’t where startups win or lose—but getting it wrong creates distractions you can’t afford. Pick a solution that matches your current team size and complexity, knowing you’ll likely switch once or twice as you scale.
For most startups with under 50 employees, Gusto hits the sweet spot of functionality, price, and ease of use. If you’re building a distributed international team, Deel or Rippling are worth the added complexity. If you want premium benefits to compete with bigger companies for talent, Justworks takes the administrative burden off your plate while giving you access to enterprise-level coverage.
And if budget is your primary constraint? OnPay proves you don’t need to overpay for reliable payroll.
The best payroll software is the one you stop thinking about—because it just works.
Need help choosing the right tools for your startup? Check out our guides on building remote teams and startup operations.