Best Payroll Software by Industry (2026)

Restaurants have the most complex payroll requirements in small business. Tip credit rules vary by state (some states don't allow tip credits against minimum wage). Tip pooling regulations changed with the 2018 FLSA amendment. Square Payroll handles tips natively and integrates with Square POS, making it the default choice for Square-based restaurants. Gusto handles tip reporting and tip credit calculations for non-Square restaurants. OnPay is a solid third option with good hospitality support. Toast POS users should check Toast's own payroll offering before evaluating third-party tools. ADP RUN has specific hospitality features but is significantly more expensive.

Retail payroll is less complex than restaurants but has its own requirements. Commission tracking is a common need for sales staff. Multi-location businesses need consistent payroll across sites. Square Payroll works naturally for Square POS retailers. Gusto handles commission payroll and has multi-location support. Lightspeed Retail and Shopify users should check native integrations before choosing. OnPay is competitive for straightforward retail payroll. The key question for retail is whether your POS system has a native payroll integration - this can save meaningful admin time.

Construction has the most technically demanding payroll requirements. Certified payroll (required for federal and many state government contracts) means submitting weekly payroll reports in a specific format showing that workers are paid prevailing wages. This is a federal requirement under Davis-Bacon and related acts. Standard payroll software (Gusto, Patriot, OnPay) does not produce certified payroll reports natively. Construction-specific platforms like Foundation, eBacon, and Procore Payroll are built for this. Gusto can handle construction payroll for non-government-contract work and has a job costing integration with QuickBooks. For government contract work requiring certified payroll, Foundation or eBacon are the right tools. ADP RUN supports union payroll reporting and has construction-specific features at the enterprise tier.

Agencies, consultancies, law firms, and professional service businesses typically have a mix of salaried employees and 1099 contractors. Remote work means multi-state is common. Detailed time tracking is often needed for client billing (separate from payroll but related). OnPay's unified pricing for W-2 and contractors makes it especially cost-effective for contractor-heavy professional services firms. Gusto Simple covers most needs. Rippling is worth evaluating above 20 employees when IT management, app provisioning, and HR become a significant admin burden. Law firms and healthcare practices with compliance requirements should check whether providers are SOC 2 certified (Gusto, OnPay, and Rippling all are).

Nonprofit payroll has unique requirements: 403(b) retirement plans (instead of 401k), grant-funded payroll allocation (different cost centers for each grant), and sometimes a board treasurer who needs payroll visibility without full admin access. Gusto offers a nonprofit discount program and handles 403(b) through its retirement integration partners. Paychex has a specific nonprofit product with grant accounting features. OnPay is competitively priced and handles basic nonprofit payroll well. ADP RUN supports 403(b) and has grant tracking features. Check whether providers offer specific 501(c)(3) pricing before signing up - Gusto, ADP, and Paychex all have nonprofit programs with discounted pricing.

Medical practices, clinics, and healthcare agencies have payroll needs around complex shift patterns (rotating schedules, call shifts, overtime rules for healthcare workers), credential and license tracking for clinical staff, and HIPAA considerations for any patient data adjacent systems. Payroll software itself does not typically handle PHI, but payroll systems that integrate with EHR platforms need to comply with BAA requirements. OnPay and Rippling both have SOC 2 Type II certifications. Rippling's credential tracking module is useful for keeping up with nurse license renewals. For small practices (under 10 providers), Gusto or OnPay handle standard healthcare payroll without healthcare-specific complexity.