Listeria monocytogenes and Cronobacter sakazakii are two important foodborne bacterial pathogens. Bacterial endophytes, which reside in plant cells, can produce antimicrobial compounds to protect the host organism or inhibit pathogens. This study investigated the bacterial community of tropical fruits for their potential to inactivate L. monocytogenes or C. sakazakii in cantaloupe and liquid infant formula, respectively. Tropical fruits including papayas, dragon fruits, and sugar apples, were sourced from several countries. Candidate bacterial endophytes were recovered from these tropical fruits using blood agar and Reasoner's 2A (R2A) agar and tested for potential inhibition against L. monocytogenes and C. sakazakii. A total of 196 bacterial endophytes were recovered from papayas, dragon fruits, and sugar apples. Among these bacterial endophytes, 33 (16.8%) and 13 (6.6%) of them demonstrated an inhibition zone against L. monocytogenes and C. sakazakii, respectively. The inhibitory strains were identified using 16S rRNA sequencing as Bacillus spp., Enterobacter spp., Klebsiella spp., Microbacterium spp., Pantoea spp., and Pseudomonas spp. A cocktail of Pantoea spp. and Enterobacter spp. was used in challenge studies with cantaloupe and significantly reduced the number of L. monocytogenes by approximately 2.5 log 10 CFU/g. In addition, P. stewartii demonstrated antagonistic activity against C. sakazakii in liquid infant formula, i.e., it significantly decreased the number of C. sakazakii by at least 1 log 10 CFU/mL. Thus, the use of bacterial endophytes recovered from fruits and vegetables could be a promising area of research. Their use as potential biocontrol agents to control bacterial pathogens in ready-to-eat foods warrants further investigation.