Abstract Heterosis, or hybrid vigor, is a crucial driver of yield and robustness in modern hybrid breeding. However, F1 hybrid plants give rise to genetically variable F2 offspring due to the segregation of genetic material in male and female meiosis. Bioengineered clonal gametes, containing identical genetic material as the parental plant, offer an innovative route to maintain genetic heterozygosity as a component of synthetic apomixis, or as a tool in breeding to carry out polyploid genome design. In this protocol, we present methods to generate clonal gametes in hybrid tomato plants by inducing synthetic apomeiosis through the Mitosis instead of Meiosis ( MiMe ) system. This protocol can be used to implement MiMe in tomato plants of choice, and describes the methods for comprehensive assessment of plant fertility and ploidy.