The native bee Nannotrigona perilampoides Cresson (Apidae: Meliponini) has been evaluated with promising results in greenhouse pollination of Solanaceae in Mexico. However, no comparison has been done with imported bumble bees (Apidae: Bombini), which are the most common bees used for greenhouse pollination. We compared the foraging activity and fruit production of habanero pepper. Capsicum chinense Jacquin, by using N. perilampoides and Bombus impatiens Cresson in pollination cages. Both bee species collected pollen on a similar number of flowers per unit time, but N. perilampoides visited significantly more flowers per trip, lasted longer on each flower, and spent more time per foraging trip. Ambient temperature and light intensity significantly affected the foraging activity of N. perilampoides. Light intensity was the only environmental variable that affected B. impatiens. Except for the fruit set, there were not significant differences in the quality of fruit produced by both bee species; however, N. perilampoides and B. impatiens performed better than mechanical vibration for all the variables measured. The abortion of fruit caused the low fruit set produced by B. impatiens, and we speculate it might be due to an excessive visitation rate. Pollination efficiency per visit (Spear’s pollination efficiency index) was similar for both bee species in spite of the significantly lower amount of pollen removed by N. perilampoides. We suggested that the highest number of flowers visited per foraging trip coupled with adequate amounts of pollen transported, and transferred between flowers, could explain the performance of N. perilampoides as a good pollinator of habanero pepper. Our experiments confirm that N. perilampoides could be used as an alternative pollinator to Bombus in hot pepper under tropical climates.