Histological scores can estimate disease staging, allowing a standardization of the assessment of non-alcoholic fatty liver disease (NAFLD). The prediction of risk of NAFLD progression is relevant to allow the planning of interventions. To analyze the application of the Iowa NAFLD decompensation risk score, the NAFLD activity score (NAS), and steatosis-activity-fibrosis score (SAF) and to assess correlations between these scores. This is a retrospective cross-sectional study enrolling 76 individuals who underwent bariatric surgery at a tertiary university hospital. Liver biopsy was performed during procedures; histological scores were then assessed. The Iowa score was calculated using age, diabetes, and platelet count. 89.5% were female and mean age was 39.1 ± 9.6 years. Mean BMI was 38.2 ± 3.7 kg/m2. Steatosis (92.1%), hepatocellular ballooning (93.4%), lobular inflammation (93.4%), and fibrosis (97.4%) were the commonest histopathological findings. According to NAS, 22.4% had definite non-alcoholic steatohepatitis (NASH). According to SAF, 89.5% had moderate or severe NAFLD. The mean risks of NAFLD decompensation at 5, 10, and 12 years were 0.8%, 2.5%, and 2.9%, respectively. The group whose risk of decompensation was above 10% comprised 2.6% and 5.3% at 10 and 12 years, respectively. The severity assessed by SAF significantly associated with definite NASH diagnosis through NAS (p < 0.001). Iowa score did not correlate with both NAS/SAF scores. The Iowa score demonstrated that individuals with obesity present with a significant long-term risk of NAFLD-related events. There were high rates of moderate/severe forms of NAFLD assessed by NAS and SAF scores. There were no significant correlations between Iowa and NAS/SAF scores.