Cherry tomatoes, consumed worldwide, have a short shelf life and are highly susceptible to significant pre- and postharvest losses, largely due to fungal pathogens like Alternaria alternata and Fusarium oxysporum. With the growing demand for nutritious food products free from synthetic preservatives, biopreservation has emerged as a safe and reliable method for controlling fungal growth in food. Biopreservation using lactic acid bacteria (LAB), known for producing antimicrobial metabolites, presents a promising approach at both the farm and industrial scales. This study investigates the antifungal potential of Lactobacillus fermentum O1.1, an isolate obtained from orange peel, against A. alternata and F. oxysporum. The growth performance of this isolate was assessed in various plant-based media, including watermelon rind (WMR), banana peel, and orange peel, in addition to MRS medium. Among these, WMR was found to be the most supportive medium for its growth. The cell-free supernatant (CFS) of Lb. fermentum O1.1 grown in WMR medium exhibited maximum inhibition of F. oxysporum (79.1%) and A. alternata (68%). Furthermore, cherry tomatoes infected with A. alternata and treated with the WMR-based CFS showed a reduced disease incidence (DI) of 16.78 ± 0.05%, compared to 40.17 ± 4.53% DI with the MRS-based CFS. Similarly, tomatoes infected with F. oxysporum and treated with the WMR-based CFS demonstrated a DI of 10.34 ± 4.86%, in contrast to 45.67 ± 4.53% DI with the MRS-based CFS. At room temperature (25 ± 2 °C), the WMR-based CFS extended the shelf life of cherry tomatoes from 2 to 5 days and decreased fungal susceptibility, with a reduction in DI by 16.78 ± 0.05% and 10.34 ± 4.86%, respectively. These findings suggest that Lb. fermentum O1.1 has significant potential as a biopreservative agent against fungal spoilage in cherry tomatoes.