Meliponiculture and associated honey production are activities with a great potential for general use and commercialization in the Peruvian Amazon. Lack of management techniques and limited knowledge of honey quality are two factors which may hinder the implementation of meliponiculture. The present study was conducted in three communities in the Peruvian Amazon where the production and physicochemical and microbiological characteristics of honey from Melipona eburnea were evaluated at 90 days following transfer from natural to rational hives. Honey from M. eburnea was also compared with the 90-day-old honey from Melipona grandis, Melipona illota, and Melipona titania. In addition, 180-day-old honey from M. eburnea was sampled and compared with the younger 90-day-old honey. The production of honey varied from 900 to 1400 mL/colony/3 months for M. eburnea. When moisture and total sugars among the different species of Melipona were compared, no significant differences were observed. Neither were there significant differences between the M. eburnea honey at 90 and 180 days of maturation. Microbiological analyses for both treatments had values <0.3/g most probable number (MPN) of coliforms and organisms of fecal origin. Stingless bee honey can therefore be harvested after 3 months, by which time its physicochemical characteristics are stable and it is microbiologically suitable for human consumption.