Abstract Background Although the use of traditional medicine (TM) to manage health issues is frequently reported, clinical guidelines often overlook this practice. This study aimed to describe the frequency of TM use to control 3 cardiometabolic risk factors for non-communicable diseases (arterial hypertension, hypercholesterolemia, and hyperglycaemia, collectively referred to as CMRF here); and associated sociodemographic, economic, and clinical characteristics. Methods Descriptive cross-sectional study with a representative population of two health districts in Ecuador, one urban in southern Quito and one in a forested rural area with diverse ethnic groups in Esmeraldas. We included 602 individuals with at least one CMRF and calculated the proportion of those who reported regular use of TM (herbal or traditional remedies) to control their CMRF. We used a multivariable logistic regression model to calculate Odds Ratios for TM use according to sociodemographic, economic, and clinical characteristics. Results TM was commonly used to control CMRF in both sociocultural contexts (39.4% Esmeraldas, 31.1% Quito), often in combination with conventional medicine (CM). A notable percentage of people (33.9% Esmeraldas, 39.0% Quito) did not take any treatment for their CMRF, and the rest used CM alone. In both settings, education was significantly associated with TM use. While in Quito people with higher education were more likely to use TM (aOR 2.04, 95%CI 1.03-3.90), in Esmeraldas, it was more common among people without formal schooling (aOR 3.76; 95%CI 1.59-8.88) as well as those of younger age (aOR per year 0.97; 95%CI 0.95-0.99) and from Afro-Ecudorian ethnicity (aOR 2.13; 95%CI 1.02-4.45). Conclusions Traditional medicine is used by a significant portion of Ecuador’s population, highlighting the need for a more accessible and intercultural approach to healthcare. Key messages • The use of traditional medicine to address hypertension, hypercholesterolemia, and hyperglycaemia appears to be widespread in different sociocultural and economic contexts of Ecuador. • To promote intercultural health, understanding the diverse sociocultural patterns associated with the use of traditional medicine, often combined with conventional medicine, is crucial.