This study aimed to characterize lactic acid bacteria (LAB) isolated from Costa Rican agro-industrial waste and explore their bioprotective potential against Salmonella in yogurt. A total of 43 LAB isolates were identified using the 16S rRNA region. In vitro inhibition of Salmonella, Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli was determined. 15 of the 43 isolates showed a good to strong antimicrobial effect against at least two pathogens. 14 selected isolates were evaluated for antibiotic resistance, gelatinase, and hemolytic activity. The bioprotective effect of the most promising strain, Lactiplantibacillus pentosus, was assessed against Salmonella sp. during yogurt fermentation. All the isolates were resistant to vancomycin and showed variable degrees of susceptibility to other antibiotics. All of the isolates were negative for gelatinase, and 5 isolates had no hemolytic activity. A significant inhibitory effect of L. pentosus_58(6)-2I (p<0.05) against Salmonella during fermentation was found, but pathogen reduction was limited to 0.611 log CFU/mL.