Best Contractor Payroll Software in 2026 — Pay Crews, Track Hours & File Taxes

Payroll is the largest expense for most contracting businesses and the most time-sensitive. Miss a Friday payroll run and you'll hear about it Monday morning — and you may not see that crew member on Tuesday.

Add certified payroll complexity for government contracts (Davis-Bacon Act prevailing wage rules, weekly submission requirements, EEOC reporting) and 1099 management for subcontractors, and you have the most operationally demanding part of running a contracting business. Contractors deal with a workforce mix that almost no other industry faces: W-2 employees, 1099 subs, union workers on some projects, non-union on others, multi-state crews that move with the work.

Generic payroll tools handle W-2 employees fine. They fall apart the moment you add a certified payroll requirement or a subcontractor who worked three jobs across two states in the same pay period.

Here's what to look for — and which platforms actually hold up.

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What Contractor Payroll Software Needs to Handle

Before comparing tools, it's worth being precise about what construction payroll actually requires. This list is the reason you can't just use the same payroll software as your accountant's dentist office. Job costing integration. Hours need to attach to jobs and phases, not just an employee record. If you're running payroll without knowing which job each hour belongs to, your job profitability numbers are guesswork. Payroll software needs to accept time entries by job code and write labor costs back to the job record — either natively or via export to your project management tool. Prevailing wage and certified payroll. Federal and state public works projects require contractors to pay workers the prevailing wage rate for their trade in that county. The Davis-Bacon Act governs federal contracts; states have their own equivalents. Payroll software needs to support multiple pay rates per worker (different jobs can require different prevailing wage rates), generate the weekly certified payroll report (WH-347 form for federal), and track fringe benefit payments. This is non-negotiable if you bid government work. Multi-state payroll. Specialty contractors — particularly mechanical, electrical, and roofing crews — follow the work across state lines. Each state has its own withholding rates, unemployment taxes, and filing requirements. Running a crew in Nevada for two weeks while your main operations are in Arizona means payroll touches two states for that period. Your software needs to handle this without manual tax research. 1099 management for subcontractors. Most contracting businesses run a hybrid workforce. Your core crew are W-2 employees; you bring in specialty subs as 1099 contractors for specific scope. Payroll software needs to track sub payments through the year and generate 1099-NEC forms at year-end. Some platforms handle this natively; others require a separate process. Union dues and benefit tracking. Union contractors need to track and remit dues, health and welfare contributions, pension, and apprenticeship fund payments per collective bargaining agreement. These are typically computed per hour worked, by trade and union local. This is one of the harder requirements — most generic payroll tools require workarounds to handle it correctly. Direct deposit and pay card support. Construction crews often have workers who don't have traditional bank accounts. Pay cards (reloadable debit cards) are common on large projects. Your payroll platform needs to handle both direct deposit and pay card funding on the same payroll run. Mobile time entry. If your crew isn't submitting time from the field via phone, you're relying on end-of-day or end-of-week recollection. That introduces errors that compound directly into payroll costs and job cost reports. Mobile time entry — ideally GPS-verified — should feed directly into your payroll calculations.

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Top 5 Contractor Payroll Platforms in 2026

1. Gusto — Best for Small Crews Without Union or Certified Payroll Needs Pricing: Simple $40/mo + $6/user · Plus $80/mo + $12/user · Premium custom

Gusto is the most polished small-business payroll tool on the market. Setup takes under an hour, direct deposit runs in two business days (or next-day on higher plans), and the UI is genuinely easy to use. For a 5-10 person residential contractor with W-2 employees and a handful of 1099 subs, Gusto handles everything cleanly.

Strengths:

• Automated federal and state tax filing across all 50 states
• Clean 1099 contractor management — track sub payments, generate 1099-NEC at year-end
• Solid benefits administration (health, dental, 401k) if you offer crew benefits
• Integrations with QuickBooks, Xero, and time tracking tools including TSheets

  Weaknesses:

  • No native certified payroll or prevailing wage support. If you win a government contract, you're handling WH-347 manually or buying a separate tool.
  • Job costing requires exporting time data and mapping it manually in QuickBooks or a spreadsheet — there's no native job cost line.
  • Union dues tracking is not supported without significant manual configuration.
  • No construction-specific workflows or terminology — it's a horizontal payroll product. Verdict: The right choice for residential remodelers, small HVAC companies, and landscaping operations that run straightforward W-2 and 1099 payroll without public works complexity. If you ever bid a government project, you'll need to supplement.

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    2. QuickBooks Payroll — Best for QuickBooks-Dependent Operations Pricing: Core $45/mo + $6/user · Premium $80/mo + $8/user · Elite $125/mo + $10/user

    If your books live in QuickBooks, QuickBooks Payroll is the path of least resistance. The integration is native — payroll transactions post directly to your chart of accounts, job cost categories update automatically, and you're not dealing with CSV exports or sync delays.

    Strengths:

    • Deep QuickBooks integration is the strongest in the market — labor costs flow to job costing in real time
    • Same-day direct deposit on Elite plan
    • Time tracking through TSheets (now QuickBooks Time) flows directly into payroll
    • Multi-state payroll on all plans
    • Automated tax payments and filings

      Weaknesses:

      • Certified payroll requires the Elite plan plus manual configuration — it's not a built-in workflow, and the WH-347 generation is clunky compared to dedicated tools
      • Union dues and fringe benefit tracking requires workarounds through payroll deductions and additional pay items
      • Price escalates quickly with crew size — a 15-person operation on Elite runs $275+/month before accounting for QuickBooks Online itself
      • Customer support is the consistent weak point — wait times are long and construction-specific questions often go unresolved Verdict: Strong choice for contractors already invested in the QuickBooks ecosystem who value tight accounting integration over construction-specific features. Not the right fit if certified payroll is a regular requirement.

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        3. Sage 100 Contractor — Best for Mid-Size Contractors Who Need Full Job Costing Pricing: Custom (typically $300-800/month depending on modules and users)

        Sage 100 Contractor (formerly Sage Master Builder) is one of the few platforms designed specifically for the construction industry. Payroll is one module within a full construction management suite that includes job costing, project management, accounts payable, and service management.

        Strengths:

        • Certified payroll is a native, first-class feature — generate WH-347 reports, manage prevailing wage rates by trade and county, track fringe benefits separately
        • Union payroll is properly supported — CBA-driven hour calculations, multiple union locals, remittance reporting
        • Job costing integration is the tightest in the market because payroll and job costing share the same database
        • Multi-state payroll with built-in compliance updates
        • AIA billing and subcontractor lien waiver tracking (adjacent to payroll but relevant for the same back-office workflows)

          Weaknesses:

          • It's a desktop-first application with a Windows-based UI that shows its age
          • Implementation takes weeks, not hours — plan for a setup investment and training time
          • Not ideal for operations under 10-15 employees; the complexity isn't justified at small scale
          • Mobile access is limited compared to cloud-native tools
          • Cost is meaningful and requires a dedicated implementation partner for most deployments Verdict: The right tool for general contractors and specialty contractors in the $3M-$30M revenue range who run public works contracts regularly and need certified payroll, union, and job costing in one place. Not for small crews, and not for contractors who want cloud-first simplicity.

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            4. Rippling — Best for Contractors With a Mixed or Growing Workforce Pricing: Core workforce platform ~$8/user/month + payroll module add-on (custom pricing, typically $15-25/user/month all-in)

            Rippling is not a construction-specific tool — it's a modern workforce platform that combines HR, IT, and payroll in one system. For contractors who are scaling and need to manage a mix of W-2 employees, 1099 contractors, benefits, and compliance without stitching together five tools, it's worth a hard look.

            Strengths:

            • Multi-state payroll is a genuine strength — Rippling handles payroll in all 50 states with automatic compliance updates
            • 1099 contractor management is clean and integrated with the same platform as W-2 payroll
            • Strong integrations with time tracking tools, accounting platforms, and HR systems
            • Benefits administration, onboarding, and device management in one platform — relevant for contractors scaling to 20+ employees
            • Faster payroll run times than most competitors (runs in minutes vs. 30+ minutes on legacy tools)

              Weaknesses:

              • No certified payroll or prevailing wage support — this is a hard stop if you run Davis-Bacon work
              • No union payroll support
              • Job costing integration requires a third-party connection — Rippling doesn't have native construction job cost tracking
              • Pricing is modular and can escalate; get a full quote before comparing to competitors
              • Construction-specific compliance (lien waivers, contractor licensing, bonding verification) is outside its scope Verdict: A strong choice for commercial contractors without public works exposure who are scaling past 15-20 employees and need a modern HR and payroll platform that doesn't feel like it was built in 2004. If Davis-Bacon ever enters the picture, plan to supplement or switch.

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                5. Viewpoint Vista — Best for Large General Contractors and ENR-Tier Operations Pricing: Enterprise custom (typically $1,000-5,000+/month depending on modules and seats)

                Viewpoint Vista (now part of Trimble) is enterprise construction ERP. Payroll is one component of a platform that also covers project management, document control, subcontract management, equipment tracking, and financial reporting. It is the system of record for many of the largest general contractors in the country.

                Strengths:

                • Certified payroll is fully supported with built-in WH-347 generation, prevailing wage rate tables, and fringe benefit tracking
                • Union payroll handles multiple agreements, locals, and trade classifications natively
                • Job costing is integrated at the deepest level — every payroll transaction hits the job cost ledger in real time
                • Multi-company, multi-state payroll is standard
                • EEOC and EEO-1 reporting built in
                • Subcontractor compliance tracking (COI, lien waivers, 1099 management)

                  Weaknesses:

                  • Cost and implementation complexity put it out of reach for most contractors under $20M in revenue
                  • Implementation takes months, requires a certified partner, and involves significant internal time investment
                  • The UI is dated — it's a power tool that requires trained users, not a system crew foremen navigate themselves
                  • Cloud migration is in progress; many installations are still on-premise Verdict: The right answer for large-volume general contractors running multiple simultaneous public works projects, multi-union workforces, and complex multi-company structures. Below $10M revenue, the cost-benefit doesn't work.

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                    Certified Payroll for Government Contracts

                    If your company bids any federally funded or state-funded public works projects — roads, bridges, public buildings, schools, water treatment facilities — Davis-Bacon Act compliance is mandatory. Understanding what certified payroll actually requires will save you from a painful audit. What Davis-Bacon requires. The Davis-Bacon Act mandates that workers on federally funded construction contracts over $2,000 be paid at least the prevailing wage for their trade and geographic area. Prevailing wage rates are published by the Department of Labor and vary by trade classification (carpenter, electrician, ironworker, etc.) and county. They are updated regularly and you are responsible for using the current rates at contract award. Weekly certified payroll reports. Contractors and subcontractors on covered projects must submit a Certified Payroll Report (WH-347 form) each week to the contracting agency. The report lists every worker, their trade classification, hours worked each day, hourly rate, gross wages, deductions, and net pay — certifying under penalty of law that you paid prevailing wages. Missing or incorrect submissions create compliance exposure. Fringe benefits. Davis-Bacon prevailing wage rates include a base rate plus a fringe benefit rate. The fringe can be paid as cash (added to the hourly wage) or as bona fide benefits (health insurance, pension contributions). Your payroll software needs to track fringe payments separately and reflect them correctly on the WH-347. State prevailing wage laws. Many states have their own prevailing wage laws that apply to state-funded projects, even those below the federal threshold. California's DIR requirements, New York's Labor Law Article 8, and Illinois' Prevailing Wage Act each have their own compliance mechanics. If you operate in multiple states, you need software that maintains state-specific rate tables. EEOC and EEO-1 reporting. Federal contractors with 50 or more employees and contracts of $50,000+ must file EEO-1 reports annually, breaking down the workforce by race, ethnicity, sex, and job category. Your payroll system needs to track the required demographic data and generate the EEO-1 report format.

                    Of the five platforms reviewed above, only Sage 100 Contractor and Viewpoint Vista handle certified payroll as a native workflow. If you're running Gusto or QuickBooks Payroll and you win a government contract, you'll need a supplemental tool — LCPtracker, eMars, or a certified payroll module from your state's contracting portal.

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                    Comparison Table

                    | Feature | Gusto | QB Payroll | Sage 100 | Rippling | Viewpoint Vista |

                    |---|---|---|---|---|---|

                    | Certified payroll (WH-347) | No | Limited | Yes | No | Yes |

                    | Prevailing wage rates | No | No | Yes | No | Yes |

                    | Union payroll | No | No | Yes | No | Yes |

                    | Multi-state payroll | Yes | Yes | Yes | Yes | Yes |

                    | 1099 contractor management | Yes | Yes | Yes | Yes | Yes |

                    | Job costing integration | Manual | Native (QB) | Native | Via integration | Native |

                    | Mobile time entry | Via integration | Via TSheets | Limited | Yes | Limited |

                    | Direct deposit | Yes | Yes | Yes | Yes | Yes |

                    | Best fit (revenue) | Under $2M | Under $5M | $3M-$30M | $2M-$20M | $20M+ |

                    | Starting price | $40/mo | $45/mo | $300+/mo | Custom | Custom |

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                    Where Ontrakt Fits

                    Ontrakt is not a payroll tool. It's job management — estimates, time tracking, invoices, and job costing for field service and construction companies. But the time tracking side connects directly to payroll workflows in a way worth explaining.

                    When crew clock in and out on a job in Ontrakt, those hours are logged against the specific job record. At the end of a pay period, you can export a labor hours report by employee and job — giving your payroll processor exactly what they need to run payroll with accurate job cost allocation. No spreadsheet reconstruction, no memory-based timesheets submitted on Friday afternoon.

                    The estimate-vs-actual view on each job shows you labor hours estimated vs. hours actually logged. If a job is running 30% over on labor, you know before the job closes — not when you're reconciling a month later wondering where margin went.

                    For contractors pairing Ontrakt with Gusto or QuickBooks Payroll, the workflow is:

                    1. Crew clocks in/out on jobs in Ontrakt via mobile

                    2. End of pay period: export hours by employee and job from Ontrakt

                    3. Import into your payroll tool (or provide to your payroll processor)

                    4. Payroll runs with job-coded labor data, posting correctly to your books

                    For contractors on Sage 100 or Viewpoint who need a faster field-side estimate and job management layer without replacing their ERP, Ontrakt handles the front-end workflow while the accounting system handles the back-end payroll and financials.

                    The goal is to not lose hours between the field and the payroll run. That's where the $15-40K per year in untracked labor typically disappears — not from bad actors, but from friction in the logging process. Mobile clock-in that takes three taps on the phone already in a tech's pocket removes that friction.

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                    Get Started

                    Ontrakt's beta program includes full access to job time logs, GPS check-in, labor cost reports, and per-job labor variance reporting at no cost for six months. Apply for beta access at ontrakt.com/beta