Introduction: The role of obesity in developing metabolic alterations is related to the distribution of adipose tissue, and visceral fat predisposes people to a higher risk than subcutaneous fat. The effect of different forms of periodization of combined training is still unknown in reducing cardiometabolic risk in adults with obesity. This randomized clinical trial aims to compare the effects of 16 weeks of periodized combined training with fixed and linear increase intensities on individuals with obesity, using the visceral adiposity index (VAI) and metabolic phenotype. Methods: In total, 59 adults with obesity (61.0% female) were allocated into three groups: control (CG, 34.4 ± 6.9 years; BMI, 33.0 ± 2.5 kg.m^-2), combined training with fixed intensity (FG, 33.6 ± 8.4 years; BMI, 32.9 ± 2.3 kg.m^-2), and linear increase intensity (LG, 34.5 ± 6.0 years; BMI, 33.4 ± 2.8 kg.m^-2) in a 1:1:1 ratio. VAI equations were used with waist circumference, triglycerides, BMI, and HDL-c. The metabolic phenotype was defined by the presence of >3 abnormalities of the following: systolic/diastolic blood pressure, triglycerides, HDL-c, fasting blood glucose, and waist circumference, classified as metabolically healthy and unhealthy (MHO; MUO). Intra- and intergroup analyses were performed per protocol (PP) and intention-to-treat (ITT) using the Generalized Estimated Equations method. p < 0.10 was the level of significance adopted for interaction, and p < 0.05 was the level of significance for the isolated effect of time and/or group. Results: VAI decreased in FG (p < 0.001) in PP and ITT analyses, but not in LG in either analysis (p > 0.05). There was a higher number of MUO in FG compared to LG, only in PP, considering the effect of group analysis (p < 0.01), but not of time or group * time or ITT analyses (p > 0.05). Conclusions: Combined training with fixed intensity improved VAI but was insufficient to affect metabolic phenotype. These findings suggest minimal differences between fixed intensity and linear increase protocols in reducing the risk of metabolic complications during obesity treatment.