Agrobiodiversity results from complex environmental relationships between ecosystems and culture, and involves carrying out various production activities on farms with natural or semi-natural land cover that provides benefits to farmers derived from the local ecosystem’s structures and processes. To characterize it, we used the main agroecological structure (MAS) index, which considers two dimensions and ten analysis criteria. The first dimension incorporates plant diversity and spatial arrangement of the biological connectors, both on the farm’s perimeter – considering its relationship with the surrounding landscape – and in its interior. The second evaluates the agrobiodiverse nature of the management practices and other cultural aspects of the producer. To evaluate the ecosystem dimension of the index, it is necessary to have high-resolution images of farms and their area of influence, but in the Andean region, these can be difficult to obtain. The use of drones and other GIS tools allows both greater access to rugged areas and higher-quality images. Spatial characterization of ecological and conventional agroecosystems was carried out in the Colombian Andes; given the technical and social considerations, a quadcopter multirotor drone (Phantom 4 Pro) was selected to allow the adaptation of a Drone/GIS-based methodology to achieve the stated goals.