Obesity increases cardiovascular risk in men through several mechanisms. Among them, low-grade chronic inflammation and obesity-associated hypogonadism have been described. We aimed to study the effects of metabolic surgery on the carotid-intima media thickness through changes in inflammatory, endothelial biomarkers, and testosterone. We included 60 men; 20 submitted to laparoscopic Roux-en-Y gastric bypass (RYGB), 20 to sleeve gastrectomy (SG), and 20 to lifestyle modification (controls). Several inflammatory and endothelial biomarkers and total testosterone (TT) were measured at baseline and six months after surgery. Free testosterone (FT) was calculated, and carotid intima-media thickness (cIMT) was measured by ultrasonography. Compared to controls, cIMT decreased after surgery concomitantly with CRP, PAI-1, sICAM-1, and IL-18 (p < 0.01) and with an increase in sTWEAK (p = 0.027), with no differences between RYGB and SG. The increase in TT and FT after surgery correlated with the changes in cIMT (p = 0.010 and p = 0.038, respectively), but this association disappeared after multivariate analysis. Linear regression showed that sTWEAK (ß = −0.245, p = 0.039), PAI-1 (ß = 0.346, p = 0.005), and CRP (ß = 0.236, p = 0.049) were associated with the changes in cIMT (R2 = 0.267, F = 6.664, p = 0.001). In conclusion, both RYGB and SG induced improvements in inflammation and endothelial biomarkers that drove a decrease in cIMT compared to men with obesity who submitted to diet and exercise.