Recent advances in chemically-controlled reprogramming of specialized cells have shown the great potential of application of small chemical molecules to regulate cellular reprogramming. We investigate the effects of small compounds, by screening of chemical libraries, and with modulators of autophagy, proteases, epigenetic marks, and other enzymes, to reduce cell death, enhance cell reprogramming and improve embryogenesis yield. These small molecules are opening up the development of new biotechnological approaches for improving in vitro embryo production in breeding programs.