Cycas circinalis belongs to the cycads, which are among the world’s most threatened plant groups. In the Western Ghats of India, this species is subject to heavy harvest pressures from commercial trade and local-level retailing. To identify the effects of these threats, we assessed the status of 37 C. circinalis populations across 13 sites in the Western Ghats, identified effects of seed, leaf and pith harvest on population structure of the species and documented phenology patterns in relation to harvest. Most populations were small, and harvest had a significant impact on the population structure. Populations subject to pith harvest entirely lacked individuals > 50 cm tall. Leaf-harvested populations had low levels of seedling and adult individuals. The timing and level of leaf production differed significantly across sites, suggesting variation in resilience to harvest with environmental conditions. Our results highlight the importance of protecting the remaining populations of this multi-purpose species.