Best Payroll Software for LLCs 2026 — Gusto vs. OnPay vs. ADP Run vs. Patriot vs. Paychex Flex

Data verified: 2026-05-08. Pricing changes frequently — verify against each provider's website before purchasing.

Monthly base fee

$40/month (Simple)

Contractor-only tier

$6/contractor/mo (no monthly base)

Per-employee fee

$6/employee/mo

Multi-state filing & tax guarantee

All 50 states; automatic federal, state, and local tax filing + deposits; new-hire reporting automatic; 100% tax accuracy guarantee; 4-day direct deposit (Simple), next-day/same-day ACH (Plus/Premium); S-Corp W-2 payroll and contractor 1099-NEC supported on same account

Support channels

Phone (Mon–Fri), Email, In-app chat, Priority support (Plus/Premium)

Trust signal

300,000+ businesses; 4.5★ App Store / 4.1★ Google Play; 100% tax accuracy guarantee; automatic W-2 and 1099-NEC year-end filing; QuickBooks two-way sync + Xero + 100+ integrations; contractor-only mode ($6/contractor, no base fee); Gusto Health for group health insurance; 401k via Guideline partnership (no setup fee); time tracking and PTO management built in

Key differentiator

Gusto is the most feature-complete payroll platform at the $40/mo entry point. Simple plan ($40/mo + $6/employee) handles full-service payroll with automatic federal, state, and local tax filing and deposits — every IRS and state agency is paid automatically with each payroll run. Contractor-only mode ($6/contractor/mo, no base fee) lets LLCs with only 1099 contractors avoid the monthly base entirely until they hire W-2 employees. Benefits admin is built in: health insurance via Gusto Health, 401k through Guideline (no setup fee), FSA/HSA, and commuter benefits. Plus plan ($80/mo + $12/employee) adds next-day direct deposit, team management, and enhanced onboarding. QuickBooks two-way sync, Xero, FreshBooks, and 100+ app integrations via Zapier make Gusto the default recommendation for most LLC owners — including those paying themselves a W-2 salary under an S-Corp election alongside 1099 subcontractors.

Verdict

Best overall for LLC owners: $40/mo full-service payroll with automatic tax filing, W-2 + 1099 support, built-in health + 401k, and contractor-only mode at $6/contractor — the strongest all-around offer in the category

Monthly base fee

$40/month

Contractor-only tier

Contractors included on standard plan

Per-employee fee

$6/employee/mo

Multi-state filing & tax guarantee

All 50 states; no per-state surcharge; automatic multi-state tax filing; 2-day direct deposit standard; same-day ACH available; automatic new-hire reporting; 100% accuracy guarantee — covers IRS and state penalties + interest if OnPay makes the error

Support channels

Phone (Mon–Fri), Email, Live chat

Trust signal

4.8★ G2; 4.9★ Capterra; 100% accuracy guarantee covering penalties + interest on OnPay's errors; all 50 states at no extra charge; W-2s, 1099s, and ACA/1095 forms auto-filed; QuickBooks + Xero integration; health insurance brokerage included; 401k via Vestwell; no setup fee; one plan — no upsell tiers

Key differentiator

OnPay's most valuable differentiator is its accuracy guarantee: if OnPay makes a payroll tax error, it covers the resulting IRS or state penalties and interest — not just the correction. This is materially stronger than most competitors' guarantees. At $40/mo + $6/employee, OnPay includes all-50-state filing at no per-state surcharge, W-2 and 1099 year-end filing, HR document library, offer letters, PTO tracking, and health insurance administration on a single plan with no upsell tiers. No dedicated mobile app (mobile-responsive web) is a meaningful limitation for payroll managers who approve runs from a phone. No contractor-only tier — contractors run on the standard plan at the per-person rate. Best fit: LLC owners who want transparent flat pricing, a genuine penalty-coverage guarantee, and all-state filing without per-state fees or tiered upgrades.

Verdict

Best accuracy guarantee: OnPay covers IRS/state penalties and interest if it makes a tax error — not just the correction; flat $40/mo + $6/employee with no per-state surcharges and no upsell tiers

Monthly base fee

From ~$59/month (Essential, custom pricing)

Contractor-only tier

Contractors on standard plan (no separate tier)

Per-employee fee

~$4/employee/mo (Essential)

Multi-state filing & tax guarantee

All 50 states; automatic multi-state tax filing; same-day direct deposit available; automatic new-hire reporting; tiered plans: Essential / Enhanced / Complete / HR Pro — pricing requires a custom quote; tax filing accuracy guarantee included

Support channels

Phone (24/7), Live chat, Dedicated support rep (Complete/HR Pro), In-person sales support (select markets)

Trust signal

1M+ businesses; 4.6★ App Store; 24/7 phone support; full ADP compliance library with HR advisory; workers' comp pay-as-you-go integration; background check integration; ADP Health Insurance available; 401k via ADP Retirement Services; QuickBooks and Sage integrations; wage garnishment services; job posting integration (ZipRecruiter on Enhanced+); guaranteed tax filing accuracy

Key differentiator

ADP Run is the payroll platform for LLC owners scaling quickly who want a single vendor for payroll, HR compliance, benefits, workers' comp, and background checks. Essential (~$59/mo base) includes full-service payroll, tax filing, and direct deposit. Enhanced adds wage garnishment services and ZipRecruiter integration. Complete adds HR advisory services and an employee handbook builder. HR Pro adds legal assistance and a dedicated HR advisor. ADP does not publish per-employee pricing — quotes are custom, which creates friction for price-comparison shoppers. The 24/7 phone support is unmatched at the Essential tier. QuickBooks integration is strong; Xero integration is limited. Best fit: LLCs with 5–50 employees in compliance-heavy industries — construction, healthcare, and multi-state professional services — where payroll is one component of a broader HR and compliance need.

Verdict

Best for compliance-heavy LLCs: 24/7 support, full HR advisory, workers' comp integration, and background check services — the enterprise-grade option for growing LLC employers in construction, healthcare, and professional services

Monthly base fee

$17/month (Basic) · $37/month (Full Service)

Contractor-only tier

Contractors included on standard plan

Per-employee fee

$4/employee/mo (both plans)

Multi-state filing & tax guarantee

All 50 states; Full Service plan: automatic federal + state tax filing; Basic plan: self-file (you make your own 941/940 deposits); additional state on Basic: +$12/mo per state; 4-day direct deposit; new-hire reporting automatic on Full Service; 100% accuracy guarantee on Full Service only

Support channels

Phone (Mon–Fri), Email, Live chat

Trust signal

4.8★ G2; 4.5★ Capterra; fully transparent pricing published online — no custom quote required; $17/mo Basic or $37/mo Full Service + $4/employee — the lowest published per-seat rate in the category; QuickBooks integration; payroll journal entry export; no long-term contracts; U.S.-based support team; 1099-NEC and W-2 filing available at year-end

Key differentiator

Patriot Payroll is the lowest-cost full-service payroll platform in the comparison with fully transparent pricing published on its website: $17/mo + $4/employee (Basic, you file your own payroll taxes) or $37/mo + $4/employee (Full Service, Patriot files and deposits for you). For an LLC with 3 employees on Full Service, total cost is $49/mo — roughly half of Gusto and OnPay at the same headcount. The $4/employee per-seat rate is the lowest in this comparison. Trade-offs: no dedicated mobile app, no native benefits administration (manage health insurance separately), no R&D credit support, limited Xero integration, and deeper QuickBooks sync is available on other platforms. The Basic plan at $17/mo is for LLC owners comfortable filing their own 941, 940, and state payroll tax returns. Full Service at $37/mo is the right default for most. Best fit: price-sensitive solo LLCs and micro-businesses with 1–5 employees where cost discipline is the primary constraint.

Verdict

Best budget option: $37/mo Full Service + $4/employee is the lowest all-in full-service payroll cost in the category — transparent published pricing, no contracts, and U.S.-based support

Monthly base fee

From ~$39/month (Essentials, custom pricing)

Contractor-only tier

Contractors on standard plan (no separate tier)

Per-employee fee

~$5/employee/mo (Essentials)

Multi-state filing & tax guarantee

All 50 states; automatic multi-state tax filing; same-day direct deposit (Essentials: next-day); automatic new-hire reporting; payroll tax accuracy guarantee; tiered plans: Essentials / Select / Pro — custom pricing required; dedicated payroll specialist assigned at every tier

Support channels

Phone (24/7), Live chat, Named dedicated payroll specialist, Paychex HR advisor (Pro tier), In-person representatives (select markets)

Trust signal

730,000+ business clients; 4.7★ App Store / 4.5★ Google Play; 24/7 phone support with a named dedicated payroll specialist; 160+ years in payroll and HR; Paychex insurance agency for group health; Paychex 401k; workers' comp pay-as-you-go; ACA compliance support; learning management system; QuickBooks integration; W-2 and 1099 year-end auto-filed

Key differentiator

Paychex Flex is the incumbent choice for mid-market LLCs that want a single HR + payroll + benefits vendor with local representative support. The Essentials plan (~$39/mo + ~$5/employee) includes full-service payroll, tax filing, and direct deposit. Select and Pro tiers add dedicated HR advisors, compensation management, and employment practices liability insurance (EPLI). Paychex does not publish transparent per-employee pricing — every quote is custom, which is a friction point. The named dedicated payroll specialist at every tier differentiates Paychex: you call one person (not a queue) when something goes wrong. Health insurance, 401k, workers' comp, and time-and-attendance are all in the Paychex ecosystem. Limited Xero integration. Best fit: restaurant, construction, and retail LLCs with 5–100 employees that value a named human contact over software self-service.

Verdict

Best for white-glove support: named dedicated payroll specialist at every tier + 24/7 phone + in-person reps in select markets — the full-service HR partner for restaurant, construction, and retail LLCs

Monthly base fee

$35/month

Contractor-only tier

$6/contractor/mo (no monthly base)

Per-employee fee

$6/employee/mo

Multi-state filing & tax guarantee

All 50 states; automatic federal, state, and local tax filing; 2-day direct deposit; tip and hours data import directly from Square POS; automatic new-hire reporting; tax accuracy guarantee; instant pay via Cash App for workers without direct deposit

Support channels

Phone (Mon–Fri), Email, In-app support, Square Seller Community

Trust signal

4.9★ App Store (Square for Restaurants); direct Square POS integration — tips, clock-ins, and sales data flow automatically into payroll; contractor-only plan ($6/contractor/mo, no base fee); W-2 and 1099-NEC auto-filed; health insurance via SimplyInsured; workers' comp pay-as-you-go; Cash App instant pay for workers without direct deposit; seamless with Square for Restaurants, Square Appointments, and Square POS

Key differentiator

Square Payroll is purpose-built for businesses already in the Square ecosystem — restaurants, retailers, food trucks, salons, and service businesses using Square POS. Hours, tips, and sales data flow automatically from Square POS into payroll, eliminating manual data entry and the compliance risk of miscalculating overtime on tip-inclusive wages. At $35/mo + $6/employee, it is the most affordable option for Square businesses. Contractor-only plan at $6/contractor/mo (no base fee) works for gig-style businesses with no W-2 employees. Cash App integration allows instant pay for hourly workers who may not have bank accounts. No native QuickBooks or Xero integration — a meaningful limitation for businesses outside the Square ecosystem. Best fit: restaurant, food truck, salon, and retail LLCs already on Square POS that want payroll synchronized with point-of-sale data.

Verdict

Best for Square POS users: automatic tip/hours import eliminates data-entry errors; $35/mo + $6/employee with contractor-only mode at $6/contractor — the natural choice for restaurant, retail, and salon LLCs on Square

Monthly base fee

From ~$8/employee/mo (Unity, custom pricing)

Contractor-only tier

Contractors included in HR Cloud

Per-employee fee

~$8+/employee/mo (all-inclusive, custom)

Multi-state filing & tax guarantee

All 50 states + global EOR in 185+ countries; automatic multi-state tax filing; same-day payroll runs available; automatic new-hire reporting; Section 41 R&D payroll-tax-offset routing built in; full tax accuracy guarantee; unified HRIS + payroll + IT + spend management platform

Support channels

24/7 Live chat, Phone support, Dedicated account manager (enterprise), Email

Trust signal

4.8★ App Store / 4.7★ Google Play; 4.9★ G2; 10,000+ businesses; built-in Section 41 R&D payroll-tax-offset routing for qualifying startups (up to $500K/yr FICA offset); employer of record (EOR) in 185+ countries; global contractor payments; unified platform: payroll + HRIS + IT device management + spend cards + benefits admin; QuickBooks + Xero + NetSuite + Salesforce + 500+ integrations; automatic W-2 + 1099 filing; same-day payroll

Key differentiator

Rippling is the only platform in this comparison with built-in R&D payroll-tax-offset routing. For LLCs with qualifying research activities, Rippling automatically routes the Section 41 payroll-tax offset (up to $500,000/yr as of current IRS limits) to reduce FICA employer deposits — rather than requiring manual coordination between a CPA and a payroll administrator. This alone can save tens of thousands annually for software, life sciences, and engineering LLCs with qualifying R&D spend. Beyond payroll, Rippling is a unified workforce platform: HRIS, payroll, IT device management, spend management, and expense automation in one system. Global EOR in 185+ countries and global contractor payments make it the right choice for remote-first or internationally distributed LLCs. Pricing starts at ~$8/employee/mo for the Unity plan (payroll only) — custom pricing requires a demo. Best fit: VC-backed startups, software LLCs with R&D tax credit eligibility, remote-first teams, and professional services firms managing contractors and employees across multiple states.

Verdict

Best for R&D-qualifying LLCs and remote teams: built-in Section 41 payroll-tax-offset routing, global EOR in 185+ countries, and unified HRIS + payroll + IT — the clear choice for software and professional services LLCs with qualifying R&D spend

1. Determine whether your LLC actually needs payroll software — and for whom Payroll software is required in three LLC scenarios: (1) You have elected S-Corp status (Form 2553) and must pay yourself a reasonable W-2 salary — the IRS mandates payroll for S-Corp owners who perform services for the business. (2) You have hired one or more W-2 employees — payroll software handles withholding, quarterly 941 filings, FUTA deposits, and annual W-2 issuance. (3) You pay 1099 contractors and want automated W-9 collection, payment tracking, and 1099-NEC year-end filing. If your LLC is a single-member disregarded entity with no employees and no S-Corp election, you likely do not need payroll software — owner draws are not payroll. Confirm your LLC's tax classification with your CPA before purchasing payroll software.
2. Choose between Full Service and self-file based on your tolerance for tax compliance responsibility Full Service payroll (automatic tax deposits and filings) is the right choice for the vast majority of LLC owners. The platform deposits FICA, FUTA, federal income tax withholdings, and state payroll taxes on your behalf each payroll cycle and files your 941, 940, and state returns automatically. Self-file (Patriot Basic at $17/mo) saves money but transfers all deposit and filing responsibility to you — a genuine compliance risk if you miss a 941 deposit deadline. IRS failure-to-deposit penalties range from 2% (1–5 days late) to 15% (10+ days late). On a $5,000 payroll deposit that is 10 days late, the penalty is $750 — far exceeding the annual price difference between Patriot Basic and Full Service for a 3-employee LLC. Default to Full Service unless you have a specific and deliberate reason to self-file.
3. Match your platform to your business ecosystem and compliance profile Your accounting software and POS ecosystem should drive your payroll platform choice. QuickBooks users benefit most from Gusto (deepest two-way sync) or OnPay. Xero users should prioritize Gusto or Rippling. Square POS users in restaurants, retail, or salons should use Square Payroll for seamless tip and hours data flow. ADP and Paychex fit LLCs that need full HR infrastructure — job posting, onboarding, EPLI, background checks, and workers' comp — in addition to payroll. Rippling is the right call for software LLCs with R&D tax credit eligibility, international contractors, or remote teams across multiple states. Avoid platforms with no Xero or QuickBooks integration if your bookkeeper works in those tools — manual journal entries are a bookkeeping error waiting to happen.
4. Calculate your true annual payroll cost including per-employee fees and multi-state surcharges The headline monthly base fee is only part of the cost. Calculate: (monthly base fee + employee count × per-employee fee) × 12 = annual payroll cost. For an LLC with 5 employees: Patriot Full Service = ($37 + 5 × $4) × 12 = $684/yr; Gusto Simple = ($40 + 5 × $6) × 12 = $840/yr; Square = ($35 + 5 × $6) × 12 = $780/yr; OnPay = ($40 + 5 × $6) × 12 = $840/yr. Add-ons — HR advisory, benefits admin, time tracking — are excluded from these base calculations and can double total cost on premium platforms. If you operate across multiple states, Patriot Basic charges +$12/state/month, which adds $144/yr per additional state. OnPay includes all states at no surcharge, making it uniquely cost-effective for multi-state LLCs at modest headcount.
5. Set up payroll before your first pay date — registration and bank verification take 3–5 business days Payroll setup requires: (1) Your LLC's EIN (Employer Identification Number) — apply free at irs.gov/ein if you don't have one yet; the online application issues your EIN immediately. (2) State employer registration in every state where you have employees — most states require registration with the Department of Revenue and Department of Labor before running payroll there. Gusto, OnPay, and Rippling guide you through multi-state employer registration during onboarding. (3) Direct deposit authorization from each employee (voided check or routing + account number). (4) Completed W-4 forms for federal withholding allowances. Most payroll platforms take 3–5 business days to verify your bank account before processing your first payroll run. Start setup at least 2 weeks before your intended first pay date — do not wait until the day before.

• LLC Self-Employment Tax Guide — when S-Corp payroll reduces SE tax exposure→
• LLC Payroll Tax Guide — 2026 FICA, FUTA, Form 941, Form 940, W-2, and state payroll taxes→
• 1099 vs W-2 Classification Guide — decide contractor versus employee before choosing payroll software→
• Hire Your Spouse in an LLC — classify spouse payroll before choosing software→
• How to Pay Yourself from an LLC — owner draws vs. W-2 salary, S-Corp payroll mechanics, and bookkeeping→
• LLC Reasonable Compensation Guide — IRS S-Corp salary doctrine, RC benchmarks, and audit defense→
• S-Corp Election Guide — when to file Form 2553 and how it creates a W-2 payroll obligation→
• Best Business Bank Accounts for LLCs — open a business account to receive payroll ACH deposits→
• EIN Application Guide — required before running payroll or hiring W-2 employees→
• Restaurant LLC Guide — payroll, tip credit, and wage compliance for food service businesses→
• Construction LLC Guide — payroll, workers' comp, and subcontractor 1099 obligations→
• Best LLC Formation Services — form your LLC before setting up payroll→

FAQ

Payroll software for LLCs — common questions