The beneficial effects of high-intensity interval training (HIIT) and chlorella vulgaris (CV) on body composition and mitochondrial biogenesis have been shown in some mechanistic studies. This study aimed to determine the effects of CV and/or HIIT on mitochondrial biogenesis, performance and body composition among overweight/obese women. There was a significant reduction in the fat mass (FM) of the CV + HIIT group, as compared with the placebo group (P = 0·005). A marginal significant increase in body water (P = 0·050) and PPAR-γ coactivator-1α (P = 0·050) was also found only in the CV + HIIT group, as compared with the placebo. Relative (P < 0·001) and absolute (P < 0·001) VO2max, as well as Bruce MET (P < 0·001), were significantly increased in the HIIT and HIIT + CV groups. Besides, the synergistic effect of CV and HIIT on the Bruce MET increment was found (interaction P-value = 0·029). No significant changes were observed in BMI, fat-free mass, visceral fat, silent information regulator 1 and fibroblast growth factor-21. In this randomised clinical trial, forty-six overweight/obese women were assigned to four groups including CV + HIIT and HIIT + placebo groups that received three capsules of CV (300 mg capsules, three times a day) or corn starch, in combination with three sessions/week of HIIT. CV and placebo groups only received 900 mg of CV or corn starch, daily, for 8 weeks. Biochemical assessments, performance assessment and body composition were obtained at the beginning and end of the intervention. HIIT may be, therefore, effective in improving mitochondrial biogenesis, performance and body composition in overweight/obese women.