Metabolic syndrome (MetS) is increasing globally. However, there is paucity of information on its association with obesity amongst young adults in Nigeria. This study was designed to investigate the prevalence of obesity, metabolic syndrome and the different BMI-metabolic risk sub-phenotypes in a young adult Nigerian population. A total of 200 young adult Nigerians (92 males; 108 females) took part in the study. Blood pressure and anthropometric readings were taken following standard protocols and body mass index was determined. Fasting blood sample was collected and biochemical assays were done using standard protocols. Obesity and metabolic syndrome were defined by the World Health Organization and modified National Cholesterol Education Program Adult Treatment Panel III criteria, respectively. BMI-metabolic-risk sub-phenotypes were defined by the presence or absence of the metabolic syndrome within the 3 BMI groups. Obesity was found in 10.88% (5.40% males; 15.80% females) of the study population. Metabolic syndrome was found in 23.80% (27.58% males; 20.58% females) of the population while hyperglycemia (41.26%) and hypertension (36.50%) were the most common metabolic abnormalities. Amongst the overweight and obese population, 80.00% and 60.00% respectively had healthy metabolic profiles while 23.68% of the normal weight participants were metabolically unhealthy. The different BMI-metabolic-risk sub-phenotypes occurred at rates of 20.00%–80.00% within the BMI groups. The prevalence of metabolic syndrome and BMI-metabolic-risk sub-phenotypes in this young adult Nigerian population is high. These findings underscore the need for an urgent public health action in order to forestall the possibility of a looming public health crisis.