Protected areas (PAs) have long been the foundation of conservation strategies to halt biodiversity losses and ecosystem degradation. In the South Caucasus (SC), coverage of PAs increased after the collapse of the Soviet Union in 1991, yet how well biodiversity is represented in them is unknown. We utilized the PA downgrading, downsizing and degazettement (PADDD) conceptual framework and the gap analysis approach to assess how changes in the PAs of Armenia, Azerbaijan and Georgia between 1991 and 2014 have affected the representation of biodiversity. Throughout this period, vegetation formations associated with high mountain ecosystems changed (≥17% representation). Colchic lowland vegetation formations which are only present in Georgia, also changed from unrepresented (0%) to under-represented (from 0% to <17%). The effect of PADDD events on biodiversity representation varied among countries depending on the amount of area gazetted after 1991. There is an inherent bias in the expansion of PAs in the SC. Our findings could be a first step towards changing the status quo by helping conservationists to strategically allocate resources towards ecosystems that are below 17% representation. Yet this will require governments in the SC to shift their views about PAs from being only national efforts to being key pieces of a larger-scale conservation strategy.