Best overall for 1099 contractors4.8From $40/moGusto
Run 1099 contractor payments and W-2 payroll in one place. Contractor self-service portal, automatic 1099-NEC, and published pricing. No add-on fees for 1099 e-file.
Best Payroll Software for 1099 Contractors (2026)
Compare payroll software that makes paying 1099 contractors simple. Top picks for contractor payments, 1099-NEC filing, contractor portals, and mixed W-2/1099 teams.
Paying 1099 contractors means running contractor payments, tracking for year-end 1099-NEC, and often handling W-2 employees in the same system. The best tools include 1099 runs and e-file without extra fees, give contractors access to pay stubs and documents, and keep setup straightforward.
Updated for 2026
Top picks for this use case
Our top payroll picks for 1099 contractors.
Best overall for 1099 contractors4.8From $40/mo
Best value for 1099 payments4.5From $40/moOnPay
Flat pricing with 1099 contractor payments and tax forms included. One plan, no tier maze. Contractor portal and support included—ideal for teams that pay mostly or only 1099.
Best for QuickBooks + 10994.6From $30/moQuickBooks Payroll
Pay 1099 contractors and employees inside QuickBooks. Labor cost posts to jobs; 1099 runs and year-end filing available. Best if you already run your books in QuickBooks.
Compare options
Side-by-side at a glance.
| Software | Best for | Starting price | Payroll types | Standout feature | Review |
|---|---|---|---|---|---|
| Gusto | Best overall for 1099 contractors | $40/mo | W-2, 1099 | Contractor portal; 1099-NEC included | Read review |
| OnPay | Best value for 1099 | $40/mo | W-2, 1099 | Flat pricing; 1099 and e-file included | Read review |
| QuickBooks Payroll | QuickBooks users | $30/mo | W-2, 1099 | 1099 + labor in QuickBooks jobs | Read review |
Editorial guidance for this audience
What to look for when you're choosing payroll as 1099 contractors.
1099 payments and year-end forms
Your software should run contractor payments and generate 1099-NEC (and 1099-MISC where applicable) for year-end. Confirm that 1099 e-file is included—some providers charge extra. Tracking payments throughout the year so year-end is accurate is essential.
Contractor self-service
A contractor portal lets subs log in to see pay stubs, payment history, and tax documents without you sending PDFs. It reduces back-and-forth and keeps records in one place. Gusto and OnPay offer this; QuickBooks Payroll has contractor access as well.
Mixed W-2 and 1099
If you have both employees and contractors, use one system for both. Payroll treats W-2 and 1099 differently (withholding vs. no withholding, different forms). The best tools handle both in the same account and keep reporting clear.
Pricing and 1099 fees
Some providers charge per 1099 run or per form at year-end. Look for included 1099 runs and e-file so you can budget. Gusto and OnPay include 1099; QuickBooks Payroll may have 1099 e-file on certain plans—check before you commit.
Why these picks work for this use case
Why we chose these tools for 1099 contractors.
Gusto
Gusto is our top pick for 1099 contractor payroll: contractor payments and 1099-NEC are built in, the contractor portal lets subs access stubs and docs, and there's no extra fee for 1099 e-file. You can run W-2 and 1099 in one place with published pricing.
OnPay
OnPay offers strong 1099 support with flat pricing—one plan, 1099 runs and filing included. Contractor portal and support are part of the package. A solid choice if you want value and simplicity without the full Gusto feature set.
QuickBooks Payroll
If you run your books in QuickBooks, QuickBooks Payroll keeps 1099 payments and labor cost in the same system. Contractor payments post to jobs for job costing. Confirm 1099 e-file is included on your plan so year-end is straightforward.
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.