(1) Consumption of diets that are caloric dense but not nutrient dense have been implicated in metabolic diseases, in part through low-grade metabolic acidosis. Mitigation strategies through dietary intervention to alleviate acidosis have not been previously reported. Our objective is to determine the effects of pH enhancement (with ammonia) in high fat diet-induced obese mice that were fed beef or casein as protein sources compared to low fat diet-fed mice. (2) Methods: B6 male and female mice were randomized ( = 10) into eight diets that differ in protein source, pH enhancement of the protein, and fat content, and fed for 13 weeks: low fat (11% fat) casein (LFC), LF casein pH-enhanced (LFCN), LF lean beef (LFB), LFBN, high fat (46%) casein (HFC), HFCN, HF beef (HFB), and HFBN. Body weights and composition, and glucose tolerance tests were conducted along with terminal serum analyses. Three-way ANOVA was performed. (3) Results: A significant effect of dietary fat (LF vs. HF) was observed across all variables in both sexes (final body weight, fat mass, glucose clearance, and serum leptin). Importantly, pH enhancement significantly reduced adiposity (males only) and final body weights (females only) and significantly improved glucose clearance in both sexes. Lastly, clear sex differences were observed across all variables. (4) Conclusions: Our findings demonstrate metabolic benefits of increasing dietary pH using ammonia, while high fat intake per se (not protein source) is the major contributor to metabolic dysfunctions. Additional research is warranted to determine mechanisms underlying the beneficial effects of pH enhancement, and interactions with dietary fat content and proteins.