BackgroundType 2 Diabetes (T2DM) prevalence is increasing in low- and middle-income countries along with high levels of obesity which vary according to socioeconomic and contextual characteristics. We aim to estimate the prevalence of T2DM and obesity in men and women in a hard-to-reach rural area in northern Ecuador considering socio-demographic characteristics.MethodsCross-sectional descriptive study based on a population-based survey in the Eloy Alfaro health district of Esmeraldas between October 2020 and January 2022. We collected sociodemographic information and risk factors for non-communicable diseases with an adapted version of the STEPS survey, performed oral glucose tolerance tests, biochemistry and took physical measurements. We estimated the prevalence of T2DM, obesity, and calculated Odds Ratios (OR) with confidence intervals by logistic regression in Stata v.15.ResultsThe overall prevalence of T2DM was 6.8% (CI95%: 4.9–8.7), markedly higher among women compared to men (10.4%, CI95% 7.3–13.4%, compared 2.0%, CI95% 0.4–3.7% respectively). The risk of having T2DM in women was 5 times higher than in men adjusting for age, ethnicity, employment, household earnings and obesity (OR: 5.03; 95%CI: 1.68–15.01). Regarding age, the risk of T2DM increased by 6% per year (adjusted OR: 1.06; 95%CI: 1.03–1.08). Obesity prevalence was 30.8% (CI95%: 27.3–34.3), in women was nearly three times higher than in men (43.2% CI95%: 38.2–48.2, compared to 14.7% prevalence, CI95%: 10.6–18.8). Indigenous women had a lower prevalence of obesity compared with the Afro-Ecuadorian women (OR: 0.05; 95%CI: 0.02–0.18) after adjusting for age, employment status, household earnings and setting.ConclusionWe found alarming differences between the prevalence of T2DM and obesity in women and men that may be explained by gender roles, exacerbated in the rural context. Health promotion measures with a gender perspective should be adapted according to the characteristics of isolated rural contexts.