The concept of the first environmental fund in Mexico arose in 1992 during the United Nations Conference on Environment and Development (Earth Summit) in Rio de Janeiro, Brazil.

During this event, various representatives of national and international conservation organizations, as well as Mexican federal environmental authorities, identified the need to establish an autonomous and permanent organization that would guarantee stable financing in the long run and would have the capacity to raise funds from diverse national and international sources to support biodiversity conservation projects. From this meeting arose the commitments of the Mexican Government and the United States Government to contribute an endowment fund for this initiative. 

The design of FMCN was based on a two-year consultancy process in which more than 400 representatives of 250 organizations, as well as national and international institutions, participated from all over the country.