Obesity is more prevalent in black South African women than men. However, little is known about the nutrient patterns associated with body composition indices in black African women. Principle Component Analysis (PCA) was applied to 25 nutrients derived from quantified food frequency questionnaires (QFFQs) in 498 middle aged black South African women. Three nutrient patterns, the plant driven, animal driven and Vitamin C, sugar and potassium driven nutrient patterns, accounted for 59% of the variance of nutrient intake. Linear models of the body composition parameters as outcome variables indicated that a standard deviation increase in the animal driven nutrient pattern was significantly associated with increases in body mass index (BMI) (1.29 kg·m−2 (95% CI, 0.54–2.04; p = 0.001), subcutaneous adipose tissue (SAT) (26.30 cm2 (7.97–44.63); p = 0.005), visceral adipose tissue (VAT) (9.88 cm2 (5.13–14.63); p < 0.001), VAT/SAT ratio (0.01 (0.00–0.02); p = 0.018), whole body fat mass index (0.74 kg·m−2 (0.25–1.22); p = 0.003), and whole body lean mass index (0.53 kg·m−2 (0.23–0.83); p = 0.001). An increase in plant driven nutrient pattern was significantly associated with an increase in SAT of 20.45 cm2 (0.47–40.43); p = 0.045. This study demonstrates that animal driven nutrient pattern, characterised by the consumption of more animal protein and fat nutrients, similar to the western diet is associated with increased body fat and lean mass.