Background: College athletes are often overlooked for metabolic syndrome (MetS), as their increased physical activity is assumed to reduce their disease risk. However, energy or macronutrient imbalance has been shown to increase risk independent of activity. The purpose of this investigation was to assess the current dietary habits of Division III female athletes and determine their associations with body composition and MetS. Secondly, we sought to determine whether dietary intake and dietary protein source (i.e., animal- and plant-based, ABP and PBP) and quality were associated with MetS, as estimated by the Simple Method for Quantifying Metabolic Syndrome (siMS) score and the siMS risk score, and whether protein pacing was associated with body composition in Division III female athletes. Methods: Stepwise linear regression determined whether age (years), body mass (kg), body mass index (BMI; kg/m2), ABP (g/d), PBP (g/d), ABP:PBP, ratio of high-quality to low-quality ABP (ABP QR), relative energy intake (kcal/kg/d), and relative protein, carbohydrate, and fat intake (g/kg/d) were predictors of siMS score and siMS risk score. Results: Twenty-five athletes (19.6 ± 1.3 years; 65.9 ± 7.0 kg; 23.5 ± 2.0 kg/m2; ABP 71.7 ± 28.2 g/d; PBP 30.0 ± 12.2 g/d) were included in the analyses. An inverse relationship was observed between PBP and the siMS score (F1, 22 = 5.498, p = 0.028) and siMS risk score (F1, 22 = 7.614, p = 0.011). The models explained 20% and 26% of the variance in siMS score and siMS risk score, respectively. Conclusions: PBP was associated with lower MetS risk in Division III female athletes, while ABP, regardless of quality, was unrelated. These associations were independent of physical activity in this cohort of Division III female athletes.