Stingless bee honey (SB) is naturally more fluid and has higher water activity than Apis mellifera honey, which favors the presence of microorganisms. Studies on honey from different SB species are essential, as behavioral variability among Brazil’s more than 300 species can directly influence the microorganisms present in the product. This study evaluated the microbiological profile of ten honey samples from different stingless bee species collected in rural areas: Tetragonisca angustula (A), Melipona bicolor (B and C), Melipona marginata marginata (D, E, and F), and Melipona quadrifasciata quadrifasciata (G, H, I, and J), testing for coliforms, Salmonella spp., lactic acid bacteria (LAB), mesophilic microorganisms (MM), yeasts, and fungi. All samples showed <3 MPN/mL for coliforms, were negative for Salmonella spp., and demonstrated ≤1 log CFU/mL of fungi. MM colony counts ranged from 3.40 to 5.28 log CFU/mL, reflecting contamination or the product’s own microbiota, potentially characterized by LAB (counts from <3 to 4.40). The lowest count (absence of cells) occurred in the only sample refrigerated by the producer. The highest microorganism count corresponded to the lowest yeast concentration, which ranged from 3.28 to 6.31 log CFU/mL. Values above 10⁴ CFU/g, the limit set by Paraná state legislation, may indicate issues in hive management or the natural microbiota accompanying the product. Yeasts can be considered intrinsic to the product, as they are introduced through the bees’ natural foraging behavior and may be used to feed larvae. Accurate identification of these yeasts may be valuable for assessing whether their presence poses real risks to consumers, thus ensuring product safety. The observed microbiological diversity may be linked to variations in bees’ foraging behaviors and the physicochemical characteristics of the honeys. A higher acidity, a feature of this type of honey, may create an unfavorable environment for the survival of certain pathogenic microorganisms.