Payroll Software for 1099 Contractors

When you pay 1099 contractors, you don’t withhold taxes—they’re responsible for their own income and self-employment tax. You do have to track payments, issue 1099-NEC forms (typically by January 31 for the prior year), and avoid misclassification (treating employees as contractors or vice versa). Payroll software that supports 1099s keeps payment history in one place and automates 1099 generation and e-filing, reducing errors and missed deadlines.

For more on contractor payroll and classification, see our payroll for contractors guide.

• •1099 payment runs — Ability to pay contractors on a schedule (e.g. per project or monthly) and track amounts paid.
• •1099-NEC generation and e-file — Year-end forms and e-filing to IRS and state where required.
• •Contractor self-service — Portal where contractors can see payment history and download documents (optional but helpful).
• •W-2 and 1099 in one system — If you have both employees and contractors, one platform for both simplifies admin.
• •Global contractors (if needed) — If you pay contractors in other countries, look for a provider like Deel that handles multi-country payments and compliance.

Gusto and OnPay both handle W-2 and 1099 payroll with contractor self-service and 1099-NEC. QuickBooks Payroll is a fit if you already use QuickBooks for accounting. For global contractors, Deel specializes in paying contractors in 150+ countries with compliant contracts and currency handling.

See our best payroll for 1099 contractors and best payroll software for full roundups.