Husk tomatoes are used in salsa and traditional medicine to alleviate illnesses. Market demand requires husk tomato varieties with improved agronomic and physicochemical health benefits. Mutagen application alters plant genomes, creating new traits and genetic diversity. The efficacy of EMS (ethyl methanesulfonate) was examined for morphology, bioactive compounds, and phytochemical improvement. Three husk tomato genotypes representing Physalis philadelphica and Physalis ixocarpa underwent two hours of 1.4% EMS. In addition to yield and yield-related properties, total phenol, antioxidant activity, chlorophyll a and b levels in leaves and fruits, and phytochemical concentrations of Na, Mg, Ca, Mn, Fe, Cu, and K in fruits were measured. Genotype-dependent morphological changes were found. The mutants C1T6 (85 cm) and C1T7 (87.60 cm) were shorter than Control C1 (102 cm). The highest yield was 5.80 g for C1T5; Control C1 produced 3.08. The mutant C2T6 produced the most (5.99 g) compared to its control (2.85 g). Mutants had higher total phenol, antioxidant activity, and leaf/fruit chlorophyll. C1T2 had the highest antioxidant activity (1.19 ng/µL). C2T1 outperformed Control C2 at 1.54 ng/µL phenolic content. C3T2 had the highest Ca content (1822 µg/g), while Control C3 had 861.20 µg/g. Mutations altered phytochemical composition, which can be used to generate nutritionally superior husk tomato varieties. Additionally, scientists will be able to study mutants with advantageous morphological and biochemical traits, enabling extensive research. Furthermore, the mutants will serve as a genetic repository for the progression of breeding procedures.