Management intensification in cultivated, tropical forests drives changes in the microclimate that can threaten native forest flora and fauna. In this study, we use epiphytic bryophytes, known to be sensitive to microclimatic changes due to their lack of a protective cuticle and the exposed habitat, to investigate the predictive power of microclimate for changes in species richness and composition. Bryophytes were sampled from understory trees in natural forest and cacao (Theobroma cacao L.) trees in two types of cacao agroforests (natural shade trees and planted shade trees) in Central Sulawesi, Indonesia. The microclimate in the agroforests was characterised by low air humidity and high air temperature during the afternoon. Bryophyte species richness did not differ between habitat types but species composition changed markedly from the natural forest to the cacao agroforests. Although no correlation between species richness and microclimate values could be found, a series of matrix-based analyses revealed a significantly positive relationship between similarities in species composition and in maximum values for temperature and minimum values for humidity, which suggests that microclimatic changes are a good predictor for high turnover of bryophyte community composition from natural forests to cacao agroforests.