This research considered native Mayan stingless bees, Melipona beecheii, with special attention to decrease in their managed colonies. From a total of 155 beekeepers located in 60 communities, 58 were randomly selected to survey in 2011. Their experience ranged from less than one to 50 years, and initial colonies from one to 100. Both structured and open interviews were conducted. Participants generally reported they believed bees were obtaining less food, which could produce colony loss. The present and a previous survey in the Zona Maya show colony loss averages 4–5% each year. In this study, during an average of 10 years, 27 beekeepers lost none, 9 lost all, and the remainder lost 44% of their colonies. Further analysis revealed colony loss had no association with relative habitat disturbance, presumed Africanized honey bee abundance, or beekeeping experience. However, those initially with more colonies in a meliponary lost them at a greater rate, indicating competition for food. Initial colony number was near 11, but currently is near 4 per meliponary. Little colony propagation (husbandry) was the norm until recently, when initiatives including meliponiculture workshops stimulated more husbandry. Twenty-six percent of beekeepers had less than one year experience and they began meliponaries using wild colonies. Because established meliponicultors were found to very seldom rely on new wild colonies, increased husbandry efforts are necessary to offset natural mortality of managed colonies. Five meliponicultors increased their colonies over 300% in two years (40 to 123 colonies), whereas a 34% loss in nine years (480 to 206 colonies) was found among the individuals randomly surveyed.