We conducted several tests on the stingless bee Melipona quadrifasciata aiming to determine the impact of the glue used for applying radio frequency identification (RFID) tags on this bee species. The study was organized in three experimental sets, in which we evaluated the effects of a synthetic glue, a natural glue (shellac), and the effects of the bee manipulation alone (control group). We performed (i) an in vitro experiment (bioassay), in which we tested five different experimental treatments in triplicate: chip plus synthetic glue, chip plus shellac, synthetic glue, shellac, and control, totaling 150 bees (n = 30 per treatment); (ii) field experiments, in which we tested the RFID tracking system composed of RFID tags, reading units, antennas, and circuit boards; and (iii) the morphological and histochemical analyses of the flight muscles of bees collected from each experimental treatment (n = 5 per treatment) at 48 h after the beginning of bioassay. Use of the natural glue, as opposed to the synthetic glue, promoted an increase of the bees’ longevity while inhibiting detrimental impacts on their foraging activities, as observed by both the bioassay and field experiments. We found negative responses to the synthetic glue treatment combined with the electronic tags, showing that the natural glue induces less morphological damage to the flight muscles of tagged stingless bees.