FONTAGRO was established in 1998 with the aim of contributing to the sustainable management of natural resources, improving competitiveness, and reducing poverty through the development of technologies and innovations relevant to the society of its member countries.

At its inception, in 1998, it received special donations from the Canadian International Development Research Centre (IDRC) and the Inter-American Development Bank (IDB), together with capital contributions from its member countries, which enabled its establishment, and funded its first projects.

Throughout its history, the fund has played a leading role, not as a traditional fund for development research, but rather as a cooperation mechanism among countries.