Tomato (Solanum lycopersicum L.) is highly susceptible to fungal infection and aflatoxin contamination, both of which pose significant public health concerns. This study evaluated the effects of different processing methods on fungal contamination and aflatoxin levels in rotting tomato varieties obtained from three markets in Ibadan, Nigeria (Bodija, Ojo, and Oja Oba). Fresh tomatoes were subjected to natural and induced rotting and processed using four methods: milling, milling followed by boiling, milling followed by refrigeration, and refrigeration of raw samples. Fungal species were isolated and identified, while aflatoxin (AFB₁, AFB₂, AFG₁, and AFG₂) concentrations were determined using standard microbiological and chromatographic techniques. Processing significantly reduced fungal contamination across the three markets. Fungal loads ranged from 0.25 to 0.90 cfu g⁻¹ in unprocessed tomato samples but decreased to 0.01–0.30 cfu g⁻¹ following processing, particularly in samples subjected to milling combined with refrigeration. Likewise, aflatoxin concentrations declined substantially after processing. For example, AFB₁ in naturally rotting Royal tomatoes from Bodija market decreased from 0.06 µg/kg in raw samples to 0.01 µg/kg after milling and refrigeration, while induced rotting Royal tomatoes from Ojo market decreased from 0.05 µg/kg to 0.02 µg/kg following the same treatment. Overall, processing methods involving milling combined with refrigeration or boiling were among the most effective treatments for reducing fungal growth and aflatoxin contamination in rotting tomatoes. These findings demonstrate the potential of appropriate processing techniques to improve the microbiological safety of tomato products, although further studies are required to optimise these methods and evaluate their long-term effects.