Abdominal obesity has emerged globally as a major public health issue due to its high prevalence and morbidity. The benefits of physical exercise among the obese population are well documented. However, the optimal exercise intensity for reducing body fat and preventing insulin resistance and metabolic disorders is still under debate. This study aimed to examine the effects of three different intensities of combined endurance and strength training programs on anthropometric variables, physiological and muscular adaptations, and insulin sensitivity. Forty-three obese young women (age 26.4 ± 4.7 years, BMI 33.1 ± 2.5 kg/m2) were randomly assigned to one of four groups: a control group (G0), a moderate-intensity training group (G50, exercising brisk walking at 50% heart rate reserve HRR), a high-intensity training group (G75, exercise jogging at 75% HRR), and an alternated-intensity training group (G50/75, exercise brisk-walking/jogging at 50−75% HRR) with additional strength training once a week for each group. Body composition, waist circumference (WC), fasting blood glucose, insulin sensitivity and resistance (Homa-IR), resting heart rate (RHR), 6-min walk distance (6MWD), 1-repetition maximum (1-RM), and time to exhaustion (TTE) at 45% and 75% maximal voluntary contraction (MVC) for both the flexor and extensor muscle groups of the knees, were recorded before and after three months of exercise training. All training groups showed significant decreases in body mass, BMI, total body fat, body fat percentage, WC, abdominal and visceral mass (p < 0.001), with a greater reduction of body mass and BMI in G75 (p < 0.05). Lean mass increased significantly only in G50/75 (p < 0.05). The insulin sensitivity and Homa-IR decreased in the three training groups (p < 0.01), with greater enhanced resistance in G50 compared to G75 and G50/75 (p < 0.05). In contrast, there were no pre-post changes in all groups for fasting blood glucose (p > 0.05). 1-RM and TTE of the knee flexor and extensor muscles were improved in the three groups (p < 0.01), with greater improvement in G50/75 for 1RM and G75 in most of the TTE parameters (p < 0.05). RHR decreased and 6MWD increased significantly in the three training groups (p < 0.01), with greater 6MWD improvement in G75 (p < 0.05). In conclusion, the three training intensities seem to generate benefits in terms of body composition, physiological and muscular adaptations, and insulin resistance. High training intensity resulted in greater improvements in body mass, BMI, and endurance and strength, whereas moderate training intensity resulted in greater improvements of insulin resistance and homo-IR. Following alternate-intensity training, greater improvements were observed in lean mass and maximal strength performance.