The physicochemical properties of honey from the stingless bee Scaptotrigona mexicana harvested at four, three, two, and actual years did not show significant differences in most of their physicochemical and antioxidant properties. Some properties, such as: color, pH, and titratable acidity were affected by storage temperature, being most affected at 45 °C. The concentration of polyphenols was correlated with the percentage of radical 2,2′-diphenyl-1-picrylhydrazyl scavenging activity (R² = 0.930). Honey showed an antibacterial activity against gram (+) and gram (–) bacteria, not showing inhibition of yeast and mold tested. The sensory evaluation showed that this honey had a high level of preference by consumers. Honey from S. mexicana bee can be stored for at least three years without being significantly affected by their physicochemical and antioxidant properties, and this is acceptable for marketing.