Since its inception in 1991, the Botanical Garden has sought to rescue and protect the biological corridor known as El Charco del Ingenio, which has undeniable ecological, landscape and historical value, making a substantial part of the biocultural heritage of San Miguel de Allende. This has involved a process of many years led by El Charco del Ingenio non-profit, facing both incomprehension as well as real estate and commercial interests of different kinds.

The first stage of this environmental rescue began with the acquisition of 67 hectares that today make up the Botanical Garden and its reserve areas, which have federal protection since its integration, in 2014, into the National System of Protected Natural Areas. The environmental project was expanded in 1993, when the civil association managed to get the City Council to recognize an adjoining 36 hectare property as a natural and recreational space, thus creating the Landeta Park, under the management of the Botanical Garden.

Another substantial achievement, in 2005, was the municipal declaration of an Ecological Preservation Zone for a large area around the Botanical Garden. This area comprises 392 hectares in which the priority is environmental conservation, thus limiting urban and real estate expansion on the biological corridor of El Charco del Ingenio. The association has achieved the integration and endurance of this ample protected territory into the successive municipal plans for urban development and ecological planning, defending by different means the territorial integrity of the decreed area.