Melipona beecheii pot-pollen is a natural product that has barely been studied, unlike other hive products such as honey and propolis. Its application has been reported since ancient times in traditional Mayan medicine, and it is also a functional food with high nutritional value. In the present study, samples of ethanolic pot-pollen extracts from five locations in the Yucatán Peninsula were analyzed to determine their antibacterial and antioxidant properties. All the extracts showed activity against five medically important bacteria; Pseudomonas aeruginosa and Listeria monocytogenes were the most susceptible bacteria in all samples. The evaluated antioxidant activity was higher than that reported by other studies. Palmitic, linoleic, and linolenic fatty acids and their respective ethyl ethers were detected by Gas Chromatography-Mass Spectrometry (GC-MS) in all samples in different concentrations. Based on these results, pot-pollen extract from Mama, Yucatán exhibited the best biological activities (Minimum Inhibitory Concentrations (MICs) between 6 and 40 mg/mL, EC50 DPPH 28 μg/mL, EC50 RP 30 μg/mL), which could be related to a higher content of unsaturated fatty acids and their ethyl esters. The present study demonstrates that M. beecheii pot-pollen has therapeutic potential in addition to its benefits as a nutritional supplement.