There are inconsistent findings regarding the different metabolic phenotypes of obesity and associated risk factors. This scoping review aims to provide a comprehensive summary of the literature that has evaluated the relationship between genetic, environmental, and nutritional factors and metabolic heterogeneity in obese and normal-weight individuals. This scoping review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) guidelines. A literature search was conducted in Web of Science, the MEDLINE database (PubMed), Scopus, and Google Scholar up to the beginning of April 2024. All observational studies (cross-sectional, case-control, and cohort) were included. Ninety-two studies were included. Of these studies, 20, 38, and 20 were evaluated for the association between genetic, nutritional, and environmental factors with metabolic phenotypes, respectively. Genetic background could be a significant factor in obesity's metabolic phenotypes. Unhealthy dietary patterns, physical inactivity, improper sleep habits, smoking, and alcohol consumption could be related to an increased risk of metabolic phenotypes. Environmental and nutritional factors can increase metabolic abnormalities. Metabolic phenotype categories are useful for predicting disease risk and for developing personalized diets and environmental interventions. These findings may help develop strategies to improve metabolic health.