: Background: Overweight and obesity are major risk factors for many chronic diseases, and weight-loss interventions often include systematic exercising and nutritional supplements. The purpose of this study was to determine the independent/synergistic effects of Spirulina maxima supplementation (6-week, 4.5 g/day) and a systematic physical exercise program (6 weeks/ 2 times) on body composition and cardiorespiratory fitness of overweight and obese subjects. Methods: 27 overweight and 25 obese sedentary male subjects were assigned to four interventions through a randomized double-blind, crossover controlled trial: Physical exercise program with (SE) or without (Ex) Spirulina maxima or no-exercise program with (Sm) and without (C) Spirulina maxima. Body composition and cardiorespiratory fitness parameters were taken during a maximal intensity test. Results: As compared to C group, SE, Sm and Ex groups reduced (p < 0.05) their body fat percentage while improving their maximal oxygen uptake (VO2max; r = −0.40), being obese subjects more benefited. Weight loss, time to reach fatigue and onset of blood lactate accumulation were improved in both Spirulina maxima supplemented groups, regardless the subjects’ body composition. Conclusions: Spirulina maxima supplementation synergistically improves the effects of systematic exercise in body composition and cardiorespiratory fitness parameters in overweight but mostly in obese adults.