Tomato (Solanum lycopersicum L.) fruit is an important component of daily diet. The fruit is perishable and commonly attacked by fungi during storage. Hence, it becomes imperative to enhance its shelf life and minimize its spoilage. The objectives of this study were to evaluate the efficacy of storage structures and botanicals in prolonging the shelf life of four varieties of tomato fruits under different storage conditions, determine the effects of storage conditions on nutritional composition of four varieties of tomato fruits, evaluate the efficacy of botanicals on fungal load during storage, isolate and identify fungi associated with deteriorated tomato fruits using both morphological and molecular tools and determine the degree of virulence of fungal isolates and their biomass in different carbon and nitrogen-rich media. Four varieties of tomato were used in this study: two local varieties (Hausa and Yoruba varieties) and two improved varieties (Tropimech and Roma VF varieties). Storage structures used were plastic crate, raffia basket and pot in pot refrigerator, while botanicals (wood ash of Vitellaria paradoxa, sawdust of Khaya ivonresis and Oryza sativa straw) were preservatives. Each botanical and sampled fruits from each variety were mixed in ratio 1:2 and stored accordingly. The shelf life was studied and lycopene content, proximate and mineral composition and fungal load were determined. The isolated fungi were identified using macromorphological and micromorphological features. Internal Transcribed Spacer (ITS) regions of the ribosomal DNA (rDNA) of fungi was amplified and sequenced. Pathogenicity test and frequency of occurrence for each isolate were carried out. Biomass of the isolates in response to carbon and nitrogen sources were determined. All data were analyzed using a statistical software called Statistical Package for Social Science (SPSS), version 16.00. One-way Analysis of Variance (ANOVA) was used to determine the differences within the variety. means were separated using Dunca 7 Multiple Range Test (DMRT). Univariate analysis of variation (under General Linear Model) was used to determine the interactions among the fixed factors (variety, storage and botanicals). Statistical software Origin 7.0 was used to plot the line graphs as well as bar charts. The findings from the study revealed that the shelf life of all the varieties was prolonged in pot in pot refrigerator for up to 20 days and storage structures had no significant effect on the loss of firmness at p≤0.05. Proximate analysis showed that moisture was highest (95.92%), followed by carbohydrate (9.04%) in all varieties irrespective of storage structure and botanicals. Mineral composition of all stored tomato fruits was significantly influenced by interactions between variety, storage and botanical at p≤0.05. Sawdust had higher antifungal potential than rice straw and ash by reducing the fungal loads in the tomato fruits. Aspergillus japonicus, Rhizopus oryzae, Curvularia geniculata, Fusarium proliferatum and Fusarium oxysporum were associated with spoilt tomato fruits of all the varieties. Sequencing of the ITS regions of rDNA of the isolates confirmed their identities. All the fungal isolates were pathogenic to different degrees with the local tomato varieties more susceptible than improved varieties. Curvularia geniculata occurred less frequently than other isolates. Biomass of each isolate was dependent on carbon and nitrogen sources in the media. The study concluded that pot in pot refrigerator was the only suitable structure in elongating the shelf life of tomato fruits. Sawdust was very efficacious to reduce incidence of fungal spoilage in tomato fruits, followed by rice straw. Pot in pot refrigerator and sawdust are recommended to minimize postharvest losses of tomato fruits.