The Forest and Milpa Landscape (FML) is a territory comprising 64 municipalities in the Yucatan Peninsula where the rainforest and the milpa system coexist. The ecosystems that predominate in the FML are sub-deciduous and subtropical evergreen forests, which represent an essential carbon reservoir worldwide. The use of natural resources for food security of FML families is associated with the milpa, which is a system that depends on the rainfall and the soil’s ability to retain water. Within the framework of the 2020–2030 Country Strategy of the GEF Small Grants Programme (SGP), 20 indicators associated with the FML’s resilience were evaluated through a participatory approach. The methodological route consisted of adapting the Toolkit for the Indicators of Resilience in Socio-ecological Production Landscapes and Seascapes (SEPLS). A topic that generated much concern among participants was human health. The reflection generated around this indicator recognised problems associated with water contamination by agrochemicals and changes in diet, resulting in recurrent diseases, such as diabetes, hypertension, and obesity. The solutions proposed by the small producers are linked to the sustainable management of ecosystems and education on values towards traditional and agroecological food production.