This study investigated the impacts of online and face-to-face Mat Pilates training in adults with persistent symptoms of long COVID on health outcomes. Forty-nine patients (52 ± 5.85 yr.) diagnosed with long COVID related to fatigue symptoms were randomly included in three groups: online Mat Pilates training (n = 16), face-to-face Mat Pilates training (n = 15), and a control group (n = 18) without training. Mat Pilates training was conducted three times a week for 12 weeks. Fatigue, functional capacity, anthropometrics, body composition, and cardiometabolic markers were assessed before and after the interventions. Two-factor Generalized Estimating Equation analyses identified significant differences with Bonferroni post hoc testing (p < 0.05). After the intervention, only the face-to-face Mat Pilates training group had an improved total, physical and mental fatigue, trunk isometric strength, upper limb muscle endurance strength, and aerobic capacity (p < 0.05). No changes were found in fat mass, muscle mass, free fat mass, % of fat, body mass, body mass index, or waist and hip circumferences. No significant changes were observed in blood glucose, glycated hemoglobin, triglycerides, total cholesterol, high-density lipoprotein, low-density lipoprotein, or blood pressure (p > 0.05). Our results highlight the potential of face-to-face Mat Pilates training as an effective intervention to mitigate persistent symptoms of long COVID related to fatigue and functional capacities.