Yes, you can pay 1099 contractors through payroll. You just need to make sure that they’re properly classified as a 1099 contractor when you onboard them to your system. Collect IRS Form W-9 from your contractors, and make sure you’re not withholding taxes when you pay them. If you pay an independent contractor more than $600 in a calendar year, your payroll software can automatically generate a 1099 form for you, the contractor, and the IRS. Gusto is one of the best ways to pay contractors through payroll. They offer a contractor-only plan that supports unlimited payments for just $6 per contractor.