•Characterization of honey by the stingless bees produced in the semi-arid region of the Brazilian northeast.•Concentration of carboxylic acids and physic-chemistry parameters were used in the evaluation.•Analysis of principal components and hierarchical cluster analysis was performed. The physicochemical characteristics of honey vary according to bee species, climate, region, period of collection, processing and storage. In this context, this work aimed to perform a comparative study of the physicochemical characteristics of Melipona subnitida and M. fasciculata honey collected at different periods and regions of the State of Piauí, Brazil. Twenty-nine honey samples were collected and evaluated by principal component analysis from physicochemical analysis data. Twenty-two percent of the parameters analyzed differed between species. Evaluating the collection period, the honey of M. subnitida and M. fasciculata presented differences among themselves. The study revealed a similarity between the physicochemical parameters of the honey of the two species of bees, in addition, the time was one of the determining factors in the formation of clusters.