We recently reported that protein-pacing (P; six meals/day @ 1.4 g/kg body weight (BW), three of which included whey protein (WP) supplementation) combined with a multi-mode fitness program consisting of resistance, interval sprint, stretching, and endurance exercise training (RISE) improves body composition in overweight individuals. The purpose of this study was to extend these findings and determine whether protein-pacing with only food protein (FP) is comparable to WP supplementation during RISE training on physical performance outcomes in overweight/obese individuals. Thirty weight-matched volunteers were prescribed RISE training and a P diet derived from either whey protein supplementation (WP, n = 15) or food protein sources (FP, n = 15) for 16 weeks. Twenty-one participants completed the intervention (WP, n = 9; FP, n = 12). Measures of body composition and physical performance were significantly improved in both groups (p < 0.05), with no effect of protein source. Likewise, markers of cardiometabolic disease risk (e.g., LDL (low-density lipoprotein) cholesterol, glucose, insulin, adiponectin, systolic blood pressure) were significantly improved (p < 0.05) to a similar extent in both groups. These results demonstrate that both whey protein and food protein sources combined with multimodal RISE training are equally effective at improving physical performance and cardiometabolic health in obese individuals.