Safety Barrier Certificates that ensure collision-free maneuvers for teams of differential flatness-based quadrotors are presented in this paper. Synthesized with control barrier functions, the certificates are used to modify the nominal trajectory in a minimally invasive way to avoid collisions. The proposed collision avoidance strategy complements existing flight control and planning algorithms by providing trajectory modifications with provable safety guarantees. The effectiveness of this strategy is supported both by the theoretical results and experimental validation on a team of five quadrotors.