Agroforestry systems can play an important role in mitigating the effects of climate change given their capacity to increase tree diversity and to store more carbon than conventional farming. This study aims at assessing carbon stocks and the use of shade trees in different coffee growing systems in the Northeast Peruvian Amazon. Carbon stocks in trees were estimated by field-based measurements and allometric equations. Carbon stocks in dead wood, litter and soil (upper 60 cm) were determined using field sampling and laboratory analysis. The diversity analysis drew on the Shannon–Weiner diversity index, and focus groups were used to obtain information about the local use of shade trees. The total carbon stock in the polyculture-shaded coffee system was 189 t C/ha, while the Inga-shaded and unshaded systems totalled 146 and 113 t C/ha, respectively. The soil compartment contributed the largest carbon stock in the coffee growing systems and contained 67, 82 and 96% of the total carbon stock in the polyculture-shaded, Inga-shaded and unshaded coffee systems, respectively. The Shannon–Weiner index and tree species richness values were highest for the polyculture-shaded coffee system, with a total of 18 tree species identified as important sources of fodder, food, wood, firewood and medicine. Therefore, coffee agroforestry systems play a significant role in carbon storage, while promoting conservation of useful trees in agricultural landscapes in the Peruvian Amazon.