The global decline of amphibians is one of the greatest challenges in Conservation Biology. Several factors including pollution, climate change, emerging diseases and habitat destruction have accelerated the rate of decline in amphibian populations worldwide, which adds to their low representation in protected areas (PAs). In this study we assessed the level of protection of PAs for 52 species of threatened amphibians and the changes in vegetation coverage inside and outside the protected areas of the Eastern Cordillera of Colombia. Between February 2015 and January 2016 we gathered occurrences from databases, biological collections and literature. The geographical records were georeferenced and overlapped on the layers of 131 PAs and on the layers of soil coverage of the Eastern Cordillera. Our results confirmed the limited level of protection provided by PAs, where only 32 species represented in 158 out of 509 geographical records show a report within PAs, which are limited to 25 areas concentrated mainly in the central region of the Eastern Cordillera. At the same time, drastic changes are evident in the soil coverage, which for most localities with occurrences between 30 and 10 years ago, are currently composed of mosaics of fragmented forests, crops and grasslands. This study demonstrates the need to establish priority actions and efficiently generate geographical areas of protection, in terms of coverage of the distribution of threatened amphibians in the Eastern region of Colombia.