Under stress, isolated microspores are reprogrammed in vitro towards embryogenesis, producing doubled haploid plants, useful biotechnological tools in plant breeding as a source of new genetic variability, fixed in homozygous plants in only one generation. Stress-induced cell death and low rates of cell reprogramming are major factors that reduce the process yield. Knowledge gained in recent years has revealed that microspore embryogenesis initiation and progression involve a complex network of factors, whose roles are not yet well understood. Autophagy and cell-death proteases are crucial players in the response to stress, while cell reprogramming and totipotency acquisition are regulated by hormonal and epigenetic mechanisms. Auxin biosynthesis, transport and action are required for microspore embryogenesis. Initial stages involve DNA hypomethylation, H3K9 demethylation, and H3/H4 acetylation. Cell wall remodelling, with pectin de-methylesterification and AGP expression, is necessary for embryo development. We will review recent findings regarding the determinant factors underlying stress-induced microspore embryogenesis, focusing on the role of autophagy, cell death, auxin, chromatin modifications, and cell wall. Recent reports show that treatments with small modulators of autophagy, proteases and epigenetic marks reduce cell death and enhance embryogenesis initiation in several crops, opening up new possibilities for improving in vitro embryo production in breeding programs.