Tomato (Solanum lycopersicum) is a premier global crop, celebrated not only for its economic importance but also as a fundamental “well-being food” that provides essential vitamins, minerals, and potent antioxidants. This review highlights the transformative impact of CRISPR/Cas9 and next-generation precision tools, such as base and prime editing, on modern tomato breeding. Beyond functional genomics, we focus on the strategic engineering of tomato to maximize productivity through fruit size optimization and the biofortification of high-value metabolites (e.g., GABA, lycopene, and vitamins). Furthermore, we examine recent advances in developing multi-stress resilience against both biotic and abiotic challenges. A significant emphasis is placed on re-designing plant architecture and developmental traits to tailor tomato varieties for future agricultural systems, particularly indoor and vertical farming. By advanced delivery methods, CRISPR technologies offer unprecedented potential to accelerate the development of “smart” tomato, ensuring sustainable agriculture and global food security in a changing climate.