Background: Excessive caloric intake and reduced energy expenditure are associated with the onset of metabolic-associated fatty liver disease (MAFLD). The aim of this study was to probe the benefits of a low glycemic index Mediterranean diet (LGIMD) and a combined exercise program (CEP) on MAFLD by monitoring the clinical process through anthropometric measurement, body mass index (BMI), and specific biomarkers, such as the Homeostatic Model Assessment for Insulin Resistance (HOMA-IR). Methods: The study was conducted at the National Institute of Gastroenterology, ‘S. de Bellis’, Italy. Subjects were invited to join the study for 12 months. Results: 54 participants were enrolled. Joint modeling of longitudinal and time-to-event data was applied. Overall, a statistically significant direct effect of LGIMD/CEP adherence on ln (BMI), a statistically significant direct effect of LGIMD/CEP adherence on time-to-event and a strong statistically significant direct effect of log (BMI) on time-to-event were observed. In addition, a statistically significant direct effect of LGIMD/CEP adherence on ln(HOMA-IR), a statistically significant direct effect of LGIMD/CEP adherence on time-to-event and a statistically significant direct effect of ln(HOMA-IR) on time-to-event were observed. Conclusions: LGIMD/CEP significantly improved MAFLD status; in addition, longitudinal BMI and HOMA-IR were good predictors of the disappearance of diagnostic criteria for MAFLD.