We present an in-depth analysis of natural forest management practices in Costa Rica based on a new historical forestry GIS database encompassing five conservation regions in the country where selective logging has been prevalent for the last 18 years. Natural forest management refers to the selective logging practices for the production of timber in natural forest ecosystems. The study considers natural forest management plans developed following a standardized format, based on Forestry Law 7575, established in 1996. Our results show a positive aspect of forest management where a large percentage of the managed forest is still standing, contrary to other tropical countries where selective logging promotes land use change. The negative finding is that managed forest areas occur in the last remaining forest fragments outside of protected areas, which challenges the continuity of selective logging in the near and mid future due to the potential impoverishment of the isolated forest stands. The most negative aspect is the recent establishment, by law, of a very short return logging cycle (10–15 years—minimum cutting cycle) as it contradicts ecological studies showing that tropical forests require over 60 years for the forest structure and composition to return to a state similar to pre-logging states. Our results should inform decision makers and managers in conservation areas to review current policies and establish new benchmarks for sustainable forest management in the country.