Honey is a functional food used worldwide and recognized for its multiple health benefits. In the present study, the physicochemical and antioxidant properties of honey produced by two species of bees (Melipona eburnea and Apis mellifera) in two seasons were evaluated. In addition, the antimicrobial activity of honey against three bacterial strains was studied. The quality of honey analyzed by LDA (linear discriminant analysis) showed four clusters mediated by the interaction, the bee species, and the collection season resulting from a multivariate function of discrimination. The physicochemical properties of the honey produced by A. mellifera met the requirements of the Codex Alimentarius, while the M. eburnea honey had moisture values outside the established ranges of the Codex. Antioxidant activity was higher in the honey of A. mellifera, and both kinds of honey showed inhibitory activity against S. typhimurium ATCC 14028 and L. monocytogenes ATCC 9118. E. coli ATCC 25922 showed resistance to the analyzed honey.