There is no such thing as a "1099 employee." Either you are an employee or you are an independent contractor (and are paid on a form 1099). If you are truly (see below) an independent contractor, they don't owe you overtime, don't have to pay the employer share of withholding, and don't have to provide benefits--but that's only IF you are truly an independent contractor, since the law does not care about people call a thing, but rather only about what it is.An independent contractor is independent to a large degree; an employee is not. If the nonprofit can tell you what hours and where to work and can direct or manage how you do your job, you are almost certainly an employee, not independent contractor and should (unless you meet the criteria to be exempt from overtime) be paid overtime; should have them pay the employer portion of withholding; and should receive whatever benefits they provide to employees. If you believe that they have "misclassified" you and that you are actually an employee, not an independent contractor, contact your state department of labor to inquire into filing a complaint.