Periodontal surgery is widely used in dentistry to treat periodontal conditions and restore oral health. Biomolecules have been incorporated into periodontal procedures to promote healing and tissue regeneration. The EPX® Biomolecule is a nanostructure composed of chitosan, graphene, thymol, and metals, including colloidal silver nanoparticles, with potential regenerative, healing, and antiseptic properties. This study aimed to evaluate the quality of soft tissue healing following periodontal surgery assisted by EPX® Biomolecule in its pharmaceutical form as a surgical gel. An experimental Phase I clinical trial was conducted in 45 patients undergoing periodontal surgery at the University Polyclinic of the Mexicali School of Dentistry, Autonomous University of Baja California, Mexico, from February 2024 to May 2025. Following informed consent, EPX® Biomolecule surgical gel was applied intraoperatively. Healing was assessed using the Early Wound Healing Score (EHS) at 7, 14, and 28 days and compared with a control group of 45 patients treated with 0.12% chlorhexidine and selected based on procedural similarity. All patients demonstrated favorable postoperative soft tissue healing. At 7 days, the EPX® Biomolecule group showed significantly better re-epithelialization, inflammation, and overall EHS outcomes than the control group; at 14 days, a significant difference remained only for re-epithelialization, while no significant differences were observed at 28 days. No adverse reactions associated with the topical intraoperative application of EPX® Biomolecule were observed.