The sustainable use of fertilizers is vital for maintaining soil fertility, promoting plant growth and protecting the environment. The impact of bat guano on tomato plants and soil fertility compared with farmyard manure (FYM) and chemical fertilizers (CF) is not well studied. To evaluate their comparative effects, an experiment was conducted from February to May 2024 at BBAU campus. Three treatments- bat guano (BG), farmyard manure, and chemical fertilizer were applied at three graded levels (BG1- 3, FYM1- 3, CF1- 3) to 27 plants, with three control plants. Morphometric parameters including plant height, leaf width, leaf length, stem circumference, and the number of flowers and fruits were recorded and analyzed using ANOVA at a 5% confidence level. Significant variations were observed in leaf width, flower production, and fruit yield with CF3 and BG3 showing superior performance in promoting vegetative growth and yield attributes. Soil physicochemical properties and tomato fruit elemental composition, assessed by AAS, revealed the highest soil organic carbon, nitrogen and sulfur under BG3. Elemental profiling of tomato fruits highlighted BG3 and FYM3 as the most effective treatments for nutrient accumulation. CF3 produced the tallest plants, while BG3 also demonstrated strong positive effects. FYM2 achieved the maximum leaf width and leaf length showed no statistically significant differences among treatments. Control plants performed poorest across all parameters. Overall, higher doses of organic fertilizers, particularly BG3, significantly enhanced tomato growth and soil fertility, underscoring their potential as sustainable alternatives to chemical fertilizers.