Plant growth relies on the bioavailability of essential nutrients in the growth environment. Access to mineral nutrients is particularly challenging for crops cultivated in alkaline soil, and in these environments, postharvest application may be effective. Advancements in nanotechnology have provided approaches to improve the essential nutrient content of plants and shelf life of produce. Mineralisation by nanoparticles is a promising postharvest technique that can fortify the essential minerals of plants. This study investigated the role of zinc oxide nanoparticles (ZnO-NPs) as a potential nano-agent to enhance Zn content in tomato (Solanum lycopersicum L.), with ZnO-NPs at 100 mg L1 applied externally to tomatoes postharvest for 4 weeks. The assimilation of Zn into the tomato tissues was quantified by inductively coupled plasma-mass spectrometry. The main shelf life factors affecting tomato quality, including microbial spoilage, water loss and colour change, were studied. All experimental data were incorporated through the neural networks model to simulate microbial involvement in fruit spoilage. The biological spoilage factor in the shelf life of tomatoes was projected with high accuracy and a relative error of 3%. Application of ZnO-NPs was associated with 47% inhibition of microbial growth on tomatoes, which may enhance the total lycopene content by up to 6%. In addition, the Zn content of tomatoes was significantly enhanced by 17%. The results also shed light on the thermal conductivity of Zn metal, which increased the dehydration of tomatoes and improved colour maturation. This study provides vital information about the beneficial application of ZnO-NPs and their role in mineralisation to enhance the shelf life of tomatoes.