Compare payroll software for general contractors (GCs) and teams managing W-2 crews plus 1099 subcontractors across trades.
General contractors need payroll that handles W-2 crews and office staff, 1099 subcontractors across trades, and labor cost that ties to jobs or projects when you use QuickBooks. Our picks work for small and growing GC operations—from those running books in QuickBooks to teams that want an all-in-one platform or simple flat-rate payroll.
Our top payroll picks for general contractors.
Best overall for small general contractors4.8From $49/moAll-in-one payroll with 1099 support for subs, contractor self-service, and automatic tax forms. Handles W-2 and 1099 in one system. Built-in time tracking for crews. No sales cycle—good for owners and office managers running payroll.
Best for GCs using QuickBooks4.6From $30/moPayroll inside QuickBooks so labor cost flows into job costing and projects. Ideal when you run invoicing and books in QuickBooks. Pay crews and 1099 subs in the same system; time tracking can tie hours to jobs.
Best value for straightforward payroll4.5From $40/moFlat pricing and one plan. Pay W-2 employees and 1099 subcontractors with tax forms included. Simple for small teams—works with any accounting software. Support included.
Best for growing GC teams4.4From Custom pricingPayroll and HR that scale to more crews and job sites. Custom pricing and optional dedicated support. Good when you're expanding and want a full-service partner for compliance and multi-state.
Side-by-side at a glance.
| Software | Best for | Starting price | Payroll types | Standout feature | Review |
|---|---|---|---|---|---|
| Gusto | Best overall for small GCs | $49/mo | W-2, 1099 | 1099 subs; time tracking; all-in-one | Read review |
| QuickBooks Payroll | GCs using QuickBooks | $30/mo | W-2, 1099 | Labor cost in jobs; job costing | Read review |
| OnPay | Best value; straightforward payroll | $40/mo | W-2, 1099 | Flat pricing; 1099 included | Read review |
| ADP | Growing GC teams | Custom pricing | W-2, 1099, multi-state | Scale; optional dedicated support | Read review |
What to look for when you're choosing payroll as general contractors.
General contractors often have W-2 superintendents and office staff plus 1099 subs across trades (electrical, plumbing, framing, etc.). Your payroll system should handle both in one place—correct withholding for W-2, no withholding for 1099, and the right tax forms (W-2 vs 1099-NEC) at year-end. Contractor self-service lets subs view pay stubs without extra admin.
Labor cost by job or project is central to GC profitability. If you run your books in QuickBooks, payroll that posts labor to jobs (QuickBooks Payroll) keeps job costing accurate. Gusto and OnPay sync to QuickBooks but don't push cost to jobs the same way; they're still strong for running payroll and tracking who worked where.
Crew hours can be captured with mobile apps, time clocks, or manual entry. The best setup syncs hours into payroll so you're not re-entering data. Gusto has built-in time tracking; QuickBooks Payroll integrates with QuickBooks Time for time-by-job. Accurate hours support job costing and overtime compliance.
1099 subcontractors need 1099-NEC at year-end. Confirm your payroll provider includes 1099 runs and e-file without per-form fees. Running contractor payments through the same system as W-2 payroll keeps one record and simplifies reporting.
Many general contractors have an owner or office manager running payroll. Choose software that's straightforward to set up and run—published pricing, no long sales cycle, and support when you need it. Gusto and OnPay are built for self-serve; QuickBooks Payroll fits if you already use QuickBooks; ADP offers dedicated support when you're ready to scale.
How each pick fits general contractors: what to validate in a trial, with links to our full reviews and official sites.
Gusto is modern payroll software for general contractors coordinating superintendents, carpenters, and steady 1099 trades without a long enterprise purchase. Contractor self-service and automated filings keep owner-operated GC offices from living in PDFs. During your first payroll cycles, confirm deposits, job or phase tags on labor (if you track them), and clean separation between employee payroll and subcontractor payments that should not hit wage reports. Model a pay week with multi-job supers, a temp labor spike, and a long-standing framer paid 1099 to validate blended scenarios. If you allocate overhead to jobs, ensure payroll exports still match how your PM software consumes labor dollars. Add another division or benefits when retainage finally clears.
QuickBooks Payroll is payroll software GCs pick when QuickBooks already runs job costing, AIA-style billing, or internal P&L by project, and payroll must post labor straight to those jobs. One system reduces arguments between accounting and field about true burdened cost. On trial payrolls, reconcile labor to two active projects and confirm burden, workers’ comp class, and equipment allocation codes behave. Pipe in time from QuickBooks Time or another tracker so field hours, drive time, and overtime do not get retyped after the superintendent approves them. Validate multi-state setups if you chase regional work. Trusted job cost feeds protect estimates on the next negotiated contract.
OnPay is payroll software for general contractors who want predictable pricing and full-service taxes while paying large pools of subs and smaller W-2 field staff from one account. Support helps when a lien-sensitive payroll question lands the day draws are due. Use early runs to prove deposit cadence, new-hire reporting, and 1099 readiness for repeat specialty contractors. Stress a payroll with blended overtime across two concurrent jobs to see if cost dimensions you care about survive export. Confirm GL mapping to QuickBooks or another ledger if finance closes by cost code. Flat invoices matter when cash is tied up in retention.
ADP belongs on the payroll software short list for general contractors scaling across states, joint ventures, or union-heavy verticals that need serviced compliance depth. Quoted programs bring implementation rigor for complex earning codes and reporting packages owners demand. After go-live, audit tax accounts for every jurisdiction where you temporarily park crews, not just your home office. Validate multi-entity or intercompany labor allocations if you use siloed LLCs per project. If certified payroll is routine, walk sample outputs with ADP before agencies compare them to your certified apps. Compare total serviced cost once those checkpoints pass.
Head-to-head comparisons to narrow your choice.
Gusto and QuickBooks Payroll both handle W-2 and 1099 payroll with automatic tax filing, but they target different workflows. Gusto is a sta…
Compare →Gusto and OnPay both serve small businesses with payroll, tax filing, and benefits, but they take different approaches. Gusto offers more HR…
Compare →Gusto and ADP both offer payroll, tax filing, and HR, but they serve different scales. Gusto is built for small businesses with transparent…
Compare →
ADP and Paychex are two of the largest full-service payroll and HR providers. Both use custom pricing and serve small business through enter…
Compare →For more options across all use cases, see our best payroll software roundup. To compare platforms side-by-side, see our payroll software comparisons.
Quick answers for this use case.
