A population-based cross-sectional study was carried out in the northern neighbourhoods of Ouagadougou (Burkina Faso), to examine the relationship of nutritional deficiencies and cardiometabolic risk factors (CMRF) with lifestyle in adults. We randomly selected 330 households stratified by income tertile. In each income stratum, 110 individuals aged 25–60 years and having lived in Ouagadougou for at least 6 months were randomly selected. We performed anthropometric, dietary intake and physical activity measurements, and blood sample collection. Cluster analysis of dietary intake identified two dietary patterns: ‘urban’ (29 % of subjects) and ‘traditional’ (71 %). The ‘urban’ cluster exhibited a higher intake of fat and sugar, whereas a higher intake of plant protein, complex carbohydrate and fibre was observed in the ‘traditional’ pattern. Female sex, low income and lack of education were associated with the ‘traditional’ cluster, as well as Fe and vitamin A deficiency. CMRF prevalence (abdominal obesity, hypertension, hyperglycaemia, dyslipidaemia) was similar in both clusters. Subjects in the ‘traditional’ cluster spent more time in physical activity and had less sedentary time than those in the ‘urban’ cluster. ‘Traditional’ dietary pattern, low income, female sex and sedentary time were significant contributing factors to the double burden of malnutrition. The rapid nutrition transition is reflected in this co-occurrence of CMRF and nutritional deficiencies. This stresses the need for prevention strategies addressing both ends of the nutrition spectrum.