Protected areas are increasingly considered to play a key role in the global maintenance of ecosystem processes and the ecosystem services they provide. It is thus vital to assess the extent to which existing protected area systems represent those services. Here, for the first time, we document the effectiveness of the current Chilean protected area system and its planned extensions in representing both ecosystem services (plant productivity, carbon storage and agricultural production) and biodiversity. Additionally, we evaluate the effectiveness of protected areas based on their respective management objectives. Our results show that existing protected areas in Chile do not contain an unusually high proportion of carbon storage (14.9%), agricultural production (0.2%) or biodiversity (11.8%), and also represent a low level of plant productivity (Normalized Difference Vegetation Index of 0.38). Proposed additional priority sites enhance the representation of ecosystem services and biodiversity, but not sufficiently to attain levels of representation higher than would be expected for their area of coverage. Moreover, when the species groups were assessed separately, amphibians was the only one well represented. Suggested priority sites for biodiversity conservation, without formal protection yet, was the only protected area category that over-represents carbon storage, agricultural production and biodiversity. The low representation of ecosystem services and species' distribution ranges by the current protected area system is because these protected areas are heavily biased toward southern Chile, and contain large extents of ice and bare rock. The designation and management of proposed priority sites needs to be addressed in order to increase the representation of ecosystem services within the Chilean protected area system.