Background: Non-alcoholic fatty liver disease (NAFLD) is the leading cause of liver disease, affecting ~30% of the population and increasing CVD. This study aimed to explore the direct, indirect and combined effects of Mediterranean diet, NAFLD and inflammation on the 10-year CVD risk in a healthy adult population. Methods: Using baseline and 10-year follow-up data from the ATTICA study, adherence to Mediterranean diet was measured using MedDietScore, and presence of NAFLD at baseline was assessed using the fatty liver index (FLI). Participants’ 10-year CVD outcomes were recorded and C-reactive protein (CRP) was used as a surrogate marker for inflammation. The direct and indirect roles of these factors were explored using logistic regression models and the pathways between them were analysed using a structural equation model (SEM). Results: NAFLD prevalence was 22.9% and its presence was 17% less likely for every unit increase in MedDietScore. NAFLD presence at baseline was associated with increased 10-year CVD incidence (39.4% vs. 14.5%, p = 0.002), but when adjusted for MedDietScore, NAFLD was not an independent predictor of 10-year CVD risk. MedDietScore was an independent protective factor of 10-year CVD risk (OR = 0.989, 95% CI: 0.847, 0.935), when adjusted for NAFLD at baseline, age, gender, sedentary lifestyle and other confounders. Further exploration using SEM showed that MedDietScore was associated with CVD risk directly even when inflammation as CRP was introduced as a potential mediator. Conclusion: FLI as a proxy measure of NAFLD is a strong predictor of 10-year CVD risk, and this prognostic relationship seems to be moderated by the level of adherence to Mediterranean diet. Adherence to Mediterranean diet remained an independent and direct CVD risk factor irrespective of NAFLD status and CRP.