Background: Photoperiod length induces in temperate plants major changes in growth rates, morphology, and metabolism, with for example modifications in the partitioning of photosynthates to avoid starvation at the end of long nights. However, this has never been studied for a tropical perennial species adapted to grow in a natural photoperiod close to 12 h/12 h all year long. Results: We grew Coffea arabica, an understorey perennial evergreen tropical species in its natural 12 h/12 h and in a short 8 h/16 h photoperiod and we investigated its responses at the physiological, metabolic and transcriptomic levels. The expression pattern of rhythmic genes, including core clock genes was affected by changes in photoperiod. Overall, we identified 2,859 rhythmic genes, of which 89% were also rhythmic in Arabidopsis thaliana. Under short days, plant growth was reduced, and leaves were thinner with lower chlorophyll content. In addition, secondary metabolism was also affected with chlorogenic acid and epicatechin levels decreasing, and in agreement the genes involved in lignin synthesis were overexpressed and those involved in the flavanol pathway were underexpressed. Conclusions: Our results show that the 8 h/16 h photoperiod induces drastic changes in morphology, metabolites and gene expression and the responses for gene expression are similar to those observed in the temperate annual Arabidopsis thaliana species.