Objectives: This study aims to investigate the effects of a combination of soy isoflavones, 8-prenylnaringenin (8-PN), and melatonin in postmenopausal women suffering from moderate-to-severe hot flashes (HFs). Methods: A multicenter, prospective, open-label study enrolled 44 postmenopausal women suffering from moderate-to-severe HFs (≥ 5 daily or ≥ 35 weekly) to receive 54.4 mg standardized soy isoflavones (including 24.5 mg genistein and 16.3 mg daidzein), 100 µg 8-PN, and 1 mg melatonin once daily for 12 weeks. The primary clinical outcomes included changes in health-related quality of life (HRQoL) scores (Menopause-Specific QoL questionnaire [MENQoL] and Cervantes Scale) and HFs following 4 and 12 weeks of treatment. Other analyses included treatment adherence, acceptability, tolerability, and safety. Results: All of the four domains of MENQoL questionnaire significantly improved at 4 weeks (P < 0.05) and 12 weeks (P < 0.001), affecting significantly the vasomotor, psychosocial, and physical spheres (41.2%, 26.3%, and 25.0%; 12 weeks improvements, respectively). Similarly, in the menopause (39.3%) and psychic (51.7%) domains (both P < 0.05 at 12 weeks), the global score of the Cervantes Scale significantly increased at 4 weeks (18.6%) and 12 weeks (35.4%). Accordingly, moderate-to-severe HFs significantly decreased at 4 weeks compared to baseline (41.7% reduction) and further reduced at 12 weeks (76.5%), including the total number of episodes. Conclusions Food supplements containing soy isoflavones, 8-PN, and melatonin showed an early and progressive benefit for reducing clinically significant HFs and for improving HRQoL across all domains, favorably affecting postmenopausal women’s overall well-being.