(1) Background: Physical inactivity has been linked to NAFLD, and exercise has been reported as useful to reduce intrahepatic fat content in NAFLD. (2) Objectives: To assess the physical activity (PA) and fitness status after a six-month lifestyle intervention (diet and PA) in adults with NAFLD and metabolic syndrome (MetS). (3) Design: Prospective cohort analysis of data obtained between baseline and six-year parallel-group randomized trial (n = 155, aged 40-60 years old, with MetS and NAFLD). Participants were randomized into three nutritional and PA intervention groups: Conventional diet (CD); MedDiet-high meal frequency (MD-HMF); MedDiet-physical activity (MD-PA). (4) Methods: PA and fitness status were assessed using a validated Minnesota questionnaire, ALPHA-FIT test battery, accelerometers, and functional fitness score. Information related to age, gender, education level, marital status, socioeconomic status, smoking habit, and alcohol consumption were also obtained. (5) Results: The CD group had higher improvement in standing handgrip than the MD-HMF group. The MD-PA group did more modified push-up repetitions than the CD group. The MD-PA and CD groups showed higher sitting handgrip than the MD-HMF group. The MD-HMF group showed the highest decrease in aerobic capacity. The MD-PA group showed lower light intensity PA/day than the CD and MD-HMF groups. The MD-PA group showed higher moderate intensity PA than the CD and MD-HMF groups. The CD group reported more METs per day than the MD-HMF group. (6) Conclusions: Lifestyle six-month intervention with diet and regular PA improved functional fitness in middle-aged patients with NAFLD and MetS. Aerobic capacity improved in patients who followed a Mediterranean diet and regular training sessions at six months.