Bacteria are associated with many infections that affect humans and present antibiotic resistance mechanisms, causing problems in health organisations and increased mortality rates. Therefore, it is necessary to find new antibacterial agents that can act in the treatment of these microorganisms. Geopropolis is a natural product made by stingless bees, formed by a mixture of plant resins, salivary secretions, wax and soil particles, presenting a diverse chemical composition. Thus, this study aimed to evaluate antibacterial activity, antibiotic modulation and the toxicity of geopropolis extract from the stingless bees, Melipona subnitida (Ducke, 1910) and Scaptotrigona depilis (Moure, 1942) against standard and multi‐resistant Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa bacteria. Geopropolis samples were collected in a meliponary located in Camaragibe, Pernambuco, Brazil. To determine the Minimum Inhibitory Concentration (MIC) and antibiotic modulation we performed broth microdilution tests. Mortality tests were used to verify extract toxicity in the model Drosophila melanogaster. The microbiological tests showed that the M. subnitida extracts had better inhibitory effects compared to S. depilis, presenting direct antibacterial activity against standard and multi‐resistant strains. The extracts potentialized antibiotic effects, suggesting possible synergy and did not present toxicity in the model used.