The antimicrobial activity of honey depends on many factors, including its botanical origin, geographical and entomological source. The aim of this study was to evaluate and compare the antimicrobial potential of honey varieties from Apis mellifera, Hypotrigona sp. and Melipona sp. against MDR Staphylococcus aureus, Bacillus cereus, Escherichia coli, Pseudomonas aeruginosa ATCC 25783, Candida tropicalis, Candida albicans SC 5314 and Cryptococcus neoformans. By using standard microbiological procedure, the agar-well diffusion and broth microdilution methods were used to evaluate honey samples for their antimicrobial and non-peroxidase activity. Different concentrations of the honey samples showed inhibition zones diameter (mm) against the test isolates. The Minimum Inhibitory Concentrations (MICs) of the honey varieties from A. mellifera, Hypotrigona sp. and Melipona sp. ranged from 6.3-25.0%, 3.1-12.5% and 6.3-25.0% (v/v) respectively. There were no statistically significant differences between the mean MICs of honey varieties against E. coli, P. aeruginosa (ATCC 25783) and C. neoformans. Hypotrigona sp. honey had the least mean against most of the test organisms. The Minimum Biocidal Concentration (MBC) of the honey varieties from A. mellifera, Hypotrigona sp. and Melipona sp. against the test organisms varied from 6.3-50%, 3.1-25% and 12-50% (v/v) respectively. There were no significant differences between the mean MBCs of the honeys against MDR S. aureus (p=0.179), E. coli (p=0.564), P. aeruginosa (ATCC 25783) (p=0.846), and C. albicans (SC5314) (p=0.264). The honeys had some levels of non-peroxidase activity against E. coli, P. aeruginosa (ATCC 25783) and C. neoformans. This study has scientifically authenticated the potential use of stingless bee honeys from "Okotobo and Ifufu" as complementary therapeutic agents.