Background The prevalence of cardiometabolic risk factors (CMRFs) is increasing in sub-Saharan Africa and represents a serious health issue. Specific and accurate data are required to implement prevention programs and healthcare strategies. Thus, the aim of this study was to estimate the prevalence rates of CMRFs according to the level of urbanization, age and gender in Gabon. Methods A cross-sectional study was conducted using the World Health Organization’s (WHO) stepwise approach for the surveillance of chronic disease risk factors. Participants over 18 years of age, without known underlying disease, from rural and urban areas of Gabon were included. Biological and behavioral data were collected using an adapted version of the standardized WHO survey questionnaire. Results The median age was 38[28-50] years. Tobacco consumption was more frequent in rural areas than in urban areas (26.1% vs 6.2%; p < 0.01). Men were more likely to be smokers than women, in both settings (aOR: 8.0[4.9-13.5], p < 0.01). Excessive alcohol consumption (19.4% vs 9.6%; p < 0.01) predominated in rural than in urban areas. Urban dwellers were less physically active than rural people (29.5% vs 16.3%; p < 0.01). In total, 79.9% of participants aged under 54 years had a high blood pressure (HBP) while 10.6% of the younger participants had pre-hypertension. Metabolic syndrome was higher in women (21.7% vs 10.0%; p < 0.01) than in men. Furthermore, 6.4% of men and 2.5% of women had a high risk of developing coronary heart diseases in the next 10 years (p = 0.03). Finally, 54.0% of the study population had three or four risk factors. Conclusion The prevalence rates of CMRFs were high in the study population. Disparities were observed according to urban and rural areas, gender and age groups. National prevention and healthcare strategies for cardiometabolic diseases in Gabon should take into account these observed differences.