Honey produced by stingless bees (Tribe: Meliponini) is well‐known for their medicinal and antimicrobial properties from their diverse content of bioactive compounds. However, it has not been possible to fully characterize its active principles. The present systematic review is based on 117 full‐text articles. Our review highlights (1) the need to apply complementary methodologies and consolidate protocols to quantify antimicrobial activity (2) to characterize antimicrobial agents in honeys of Heterotrigona itama, Tetragonisca angustula, and Melipona beecheii, and; (3) to search for compounds against multidrug‐resistant and/or biofilm‐forming pathogens. Moreover, we performed a meta‐analysis of 29 articles with quantitative data using diffusion assays and minimum inhibitory concentration (MIC). Staphylococcus aureus and Escherichia coli were the most evaluated pathogens, evidencing 221 and 149 antimicrobial activity assays against honey samples of 36 and 24 stingless bee species, respectively. The highest pooled mean in diffusion assays against S. aureus showed a difference between methicillin‐resistant S. aureus (MRSA) and non‐MRSA strains {14.43 [95% confidence interval (CI): 12.16–16.71] mm vs. 11.55 (95% CI: 10.22–12.87) mm}, whereas E. coli showed pooled means of 9.09 (95% CI: 7.93–10.25) mm. Regarding MIC expressed as volume/volume percentage (%, v/v), the estimated inhibitory concentrations were 7.89 (95% CI: 3.94–11.83) mL/100 mL for MRSA and 5.60 (95% CI: 2.66–8.55) mL/100 mL considering all S. aureus strains. In contrast, the estimated MICs as weight/volume percentage (%, w/v) showed 15.00 [(95% CI: 12.84–17.16) g/100 mL for S. aureus and 16.17 (95% CI: 5.78–26.55) g/100 mL for E. coli. However, honey remains an unexplored source of antimicrobial molecules.