Copyright © The Authors 2017. Objective To determine the prevalence of and modifiable factors associated with prediabetes in the Comcáac Indians. Design Cross-sectional study where prediabetes was defined using fasting plasma glucose, 2 h plasma glucose and glycated Hb (HbA1c). Physical, anthropometric and biochemical measurements, medical record, socio-economic, dietary and physical activity information were collected. The modifiable factors associated with prediabetes were assessed using multiple logistic regression. Settings Comcáac Indian communities of Punta Chueca and El Desemboque, Sonora, Mexico. Subjects Adults (n 227) aged 20 years or older. Results The sex- and age-adjusted prevalence (95 % CI) of prediabetes was 47·1 (40·8, 53·5) % in the overall population; age-adjusted prevalence was 47·3 (35·6, 59·0) % in men and 46·7 (39·1, 54·3) % in women. The modifiable factors associated with a risk of prediabetes (OR; 95 % CI) were light-intensity physical activity (per 1 h/week increase: 1·04; 1·01, 1·07) and insulin resistance (homeostasis model assessment of insulin resistance score >6·1 v. <4·1: 4·62; 1·37, 15·51). Increased consumption of a traditional dietary pattern based on fish and seafood, low-fat cereals, fruits and vegetables was a protective factor (0·49; 0·31, 0·79). All variables were modelled together and adjusted for age and sex. Conclusions The high prediabetes prevalence found in the Comcáac community is alarming because it represents a large number of people who are at risk for type 2 diabetes. The identification of modifiable factors associated with prediabetes that are specific to this population may be useful for designing effective strategies to prevent prediabetes.