Non-alcoholic fatty liver disease (NAFLD) is a chronic disease with several degrees of histological features which may progress to cirrhosis. Obesity is an important risk factor and although NAFLD has no specific pharmacological treatment, bariatric surgery has been associated with NAFLD regression in severely obese patients. However, few longitudinal histological studies support this finding. Therefore, firstly, a retrospective study was performed including clinical and histological data of 895 obese patients who underwent bariatric surgery. In addition, histological analyses of 30 patient's liver biopsies were evaluated at two timepoints (T1 and T2). The retrospective analysis of the total number of patients revealed that the average body mass index (BMI) was 35.91 ± 2.81 kg/m2. The liver biopsies during bariatric surgery showed that 53.52% did not present NAFLD, 30.16% had NASH, 15.98% isolated steatosis and 0.34% liver cirrhosis. The median BMI of the longitudinal cohort decreased from 37.9 ± 2.21 kg/m2 at the time of bariatric surgery (T1) to 25.69 ± 3.79 kg/m2 after 21 ± 22 months after the procedure (T2). The prevalence of NAFLD in T1 was 50%, and 16.67% in T2. The histological area of collagen fiber was lower in T2 compared to T1 (p = 0.0152) in the majority of patients, which was also illustrated by immunohistochemistry for Kupffer cell and myofibroblast formation markers. These findings confirmed the NAFLD regression after bariatric surgery and, for the first time, showed the amelioration of these features using more accurate histopathological techniques.