The Muisca Indigenous people in Cota, Colombia, has committed to reviving and strengthening their traditional culture, including the ancestral knowledge associated with their traditional medicine. To explore the occurrence of traditional medicine and factors associated with its use among the Muisca people in Cota, Colombia. A participatory cross-sectional study applied a questionnaire to 471 Muisca mothers who had at least one child over 10 in April 2019. The 44 questions inquired demographic, social, and cultural factors of participants and their knowledge, use and practice of traditional medicine. We used the Mantel-Haenszel procedure to measure the associations using Odds Ratio and 95% confidence intervals. 66.2% (312/471) of the mothers knew at least three cases of traditional diseases; 56.8% (267/470) had and used medicinal plants; 15.8% (73/462) had practiced traditional self-care for flu, menstruation and postpartum; and 11.8% (54/458) reported that they had gone to midwives, bonesetters and healers. Four factors had a significant association (p < 0.05) with traditional medicine: consumption of three traditional foods; having traditional gardens and plants; living within the reservation; and parents born in a municipality of indigenous influence. The study showed that the permanence of traditional medicine is strongly associated with traditional food, agricultural vocation and the possession and use of medicinal plants. The results suggest that the strategy for the recovery of traditional medicine could focus on promoting a stronger link between indigenous identity, territory, food and health.