The present invention is directed generally to systems for making host cells with artificial endosymbionts. In an embodiment, the systems of the invention comprise a host cell, an artificial endosymbiont, a means for introducing the artificial endosymbiont to the host cell, a means for separating the host cells with artificial endosymbionts from free artificial endosymbionts, and a means for detecting artificial endosymbionts in host cells.