Best overall for contractors4.8From $40/moGusto
All-in-one payroll with strong 1099 support, contractor self-service, and automatic tax forms. No sales cycle—published pricing and fast setup.
Best Payroll Software for Contractors (2026)
Compare payroll software built for contractors and trade businesses. Top picks for 1099 payments, mixed W-2/contractor crews, and job-costing-friendly workflows.
Contractors and trade businesses need payroll that handles both W-2 employees and 1099 subs, keeps labor cost tied to jobs when you use QuickBooks, and doesn't add unnecessary complexity. Our picks below excel at contractor support, tax forms, and ease of use.
Updated for 2026
Top picks for this use case
Our top payroll picks for contractors.
Best overall for contractors4.8From $40/mo
Best for QuickBooks + job costing4.6From $30/moQuickBooks Payroll
Payroll inside QuickBooks so labor cost flows straight into job costing. Ideal if you already run your books in QuickBooks and pay crews and subs.
Best value for contractors4.5From $40/moOnPay
Flat pricing and straightforward 1099 runs. Contractor payments and tax forms without a tier maze. Works with any accounting software.
Compare options
Side-by-side at a glance.
| Software | Best for | Starting price | Payroll types | Standout feature | Review |
|---|---|---|---|---|---|
| Gusto | Best overall for contractors | $40/mo | W-2, 1099 | Contractor portal; 1099-NEC; all-in-one | Read review |
| QuickBooks Payroll | QuickBooks + job costing | $30/mo | W-2, 1099 | Labor cost in QuickBooks jobs | Read review |
| OnPay | Best value | $40/mo | W-2, 1099 | Flat pricing; 1099 included | Read review |
Editorial guidance for this audience
What to look for when you're choosing payroll as contractors.
1099 and mixed crews
If you pay both W-2 employees and 1099 contractors, choose a platform that handles both in one place with clear tax treatment. Contractor self-service portals let subs view pay stubs and documents without extra back-and-forth.
Tax forms and compliance
Look for automatic 1099-NEC (and 1099-MISC where applicable) and year-end filing. Some providers charge extra for 1099 e-file—confirm it's included. Multi-state contractors need a provider that handles state withholding and reporting.
Job costing and accounting
If you run job-based books in QuickBooks, payroll that posts labor to jobs saves time and keeps reporting accurate. QuickBooks Payroll does this natively; Gusto and OnPay sync to QuickBooks but don't push cost to jobs the same way.
Ease of use and support
Contractors often wear many hats. Pick payroll you can set up and run without a long sales cycle. Published pricing (Gusto, OnPay) makes comparison easier; QuickBooks Payroll fits if you're already in the ecosystem.
Why these picks work for this use case
Why we chose these tools for contractors.
Gusto
Gusto is our top pick for most contractor businesses: transparent pricing, strong 1099 support, contractor portal, and no lock-in to one accounting system. It fits mixed W-2/1099 crews and scales from a few people to dozens.
QuickBooks Payroll
When you live in QuickBooks for estimates, invoicing, and job costing, QuickBooks Payroll keeps payroll and labor cost in the same system. No sync or export—payroll posts to the right accounts and jobs. Best for contractors who already rely on QuickBooks.
OnPay
OnPay offers similar contractor-friendly features to Gusto with a simpler pricing structure: one plan, flat base plus per person. 1099 runs and support are included. A solid choice if you want value and clarity without the full Gusto feature set.
For more options across all use cases, see our best payroll software roundup. To compare platforms side-by-side, see our payroll software comparisons.
FAQs
Quick answers for this use case.