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I started a run my own nonprofit corporation. We have a board of directors and my title is executive director, founder, and am on the board. We have been completely volunteer staffed including myself and have no office now. We just received a grant to temporarily part of a salary as executive director for just 3 months, but this may or may not continue depending on our success with fundraising.

Should I be paid as a 1099 contractor or an employee? From my personal perspective and the organization perspective, which makes most sense? I've read through to understand some of the benefits of each. I also cannot determine if there is a legally correct answer.

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To be an employee (W2) or independent contractor (1099) is a legal distinction. See the IRS Independent Contractor vs. Employee?.

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You have to pay yourself as an employee if you are running the charity. It's hard to be 'independent' if you are running the place :)

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