Understanding the dynamics of crop choices in different regions is critical to designing effective strategies for sustainable agriculture and rural development. The experiment was carried out in six municipalities in the Andean region of the department of Nariño, Colombia. The correspondence analysis was used to explore the association between the preferences of farmers and cultivated fruit species. On farms of 90 fruit growers, seven Andean fruit crops were planted, including Solanum betaceum, S. quitoense, Physalis peruviana, Passiflora pinatistipula, P. ligularis, P. edulis, R. fruticosus. At the end of the experiment, a structured survey was carried out to ask the producers which crop they preferred to implement on their farm, and which one produced the worst experience. In addition, a general diagnosis of the main phytosanitary problems they had throughout the cultivation period was carried out. Arboleda and Sandoná farmers demonstrate a distinctive inclination towards S. betaceum, while Ipiales exhibits a preference for P. peruviana. Conversely, La Florida, Providencia, and El Peñol distinctly favor S. quitoense, with widespread acceptance for R. glaucus and P. ligularis. Farmers do not have a preference for planting P. pinatistipula in Ipiales. S. betaceum was intensified Anthracnosis and Potyvirus-related issues, affecting crop periods and fruit quality. S. quitoense faces altitude-dependent pathogen susceptibility, while R. fruticosus contends with downy mildew. Passion fruit confronts Fusarium sp., gray mold, and dieback. Tailored interventions are crucial for sustainable agriculture amidst diverse challenges. This research contributes valuable insights for informed agricultural planning and regional development policies.