We set out to evaluate the association between nutrient patterns and general adiposity in black South African adolescents and adults and to determine whether the interactions are longitudinally sustained over 24 months. Principal Component Analysis (PCA) was used to derive the nutrient patterns of 750 participants (250 adolescents between 13 and 17 years old and 500 adults who were 27 years or 45+ years old). PCA was applied to 25 nutrients, computed from the quantified food frequency questionnaire (QFFQ) over a 24 months period. The nutrient patterns between adolescents and adults were similar over time; however, their associations with BMI were different. Among the adolescents, only the "plant-driven nutrients pattern" was significantly associated with a 0.56% (95% CI (0.33; 0.78); p < 0.001) increase in BMI. Among the adults, the "plant-driven nutrient pattern" (0.43% (95% CI (0.03; 0.85); p < 0.001) and the "fat-driven nutrients pattern" (0.18% (95% CI (0.06; 0.29); p < 0.001) were significantly associated with a BMI increase. Furthermore, the "plant-driven nutrient pattern", "fat-driven nutrient pattern" and the animal-driven nutrient pattern revealed sex differences in their association with BMI. Urban adolescents and adults had consistent nutrient patterns, but their BMI relationships changed with age and gender, an important finding for future nutrition interventions.