The nutritional composition of dietary intake could produce specific effects on metabolic variables such as mitochondrial oxidation, whose understanding could contribute to apply more individualized weight-lowering strategies. This study assessed the effects of four hypocaloric diets with high protein content or different food distribution on metabolic changes and mitochondrial oxidation accompanying weight loss. Thirty-five obese men (body mass index of $31.8;{pm};3.0;kg/m^2$ an $38;{pm};7$ years old) were randomly assigned to one of the four treatments (8 weeks): control diet (C-diet); legume diet (L-diet) fatty fish diet (FF-diet); or high-protein diet (HP-diet). Body composition, blood pressure, resting energy expenditure, mitochondrial oxidation, blood biomarkers, and dietary intake were assessed. The HP-diet and L-diet achieved the greater body weight reduction ($-8.4;{pm};1.2%$ and $-8.3;{pm};2.9%$, respectively), as compared to the C-diet ($-5.5;{pm};2.5%$; P =.04 high-density lipoprotein cholesterol concentrations were reduced in all dietary groups except for the FF-diet. Total and low-density lipoprotein cholesterol levels were significantly improved by the L-diet (P < .05), while the homeostatic model assessmen index of insulin resistance value was significantly reduced in those men following the HP-diet. Mitochondrial oxidation was specifically activated by the HP-diet and L-diet at the end of the study. Interestingly, a lineal regression model explained about 25% (P = .029) of the mitochondrial oxidation variability as influenced by the diet changes once adjusted by resting energy expenditure. The specific consumption of legumes or high protein content within a hypocaloric diet could activate mitochondrial oxidation, which could involve additional benefits to those associated with the weight reduction.