Vigorous and stress-resistant hybrid crops are preferred in modern agriculture, yet F1 hybrid seeds must be recurrently produced as the offspring of hybrids segregate for beneficial traits due to genetic reshuffling via meiosis. The development of approaches to skip meiosis and fertilization, and produce asexual, clonal, seeds are of major agricultural interest. To date, engineered clonal gamete formation and synthetic apomixis remain to be established in any dicot crops. Herein we engineered Mitosis instead of Meiosis (MiMe) system in hybrid tomatoes where the meiotic division essentially reverts to mitotic division. Our tomato MiMe system requires the simultaneous mutation of three crucial factors required for meiotic recombination initiation (SPO11-1), sister-chromatid cohesion (REC8) and entry into the second meiotic division (TAM). We demonstrate hybrid MiMe plants give rise to unreduced and non-recombined gametes and ultimately tetraploid offspring that maintain heterozygosity genome-wide. We bioengineered the MiMe system in three hybrid genotypes and used it to establish polyploid genome design. Through the hybridization of MiMe hybrids, we generated “4-Haplotype” plants that encompass the complete genetics of their four inbred grandparents, providing a blueprint for exploiting polyploidy in crops. Remarkably, we provide evidence that pollination of hybrid MiMes with a maternal haploid inducer (Sldmp) can lead to the formation of clonal diploid, hybrid offspring inheriting genetic material exclusively from the mother. Therefore, our findings provide a foundation for novel breeding approaches in tomato, potato and other important dicot crops, which will open the door for synthetic apomixis and polyploid genome design in dicot crops.