Periapical endodontic surgery involves surgical techniques to: remove a persistent periapical lesion, clean the apex of the tooth, and facilitate access to the apical end of the root canal, which will then be retrograde filled. Intraoperative antimicrobials are important in these procedures because they prevent and treat sepsis in the area. The EPX® Biomolecule contains chitosan fortified with silver and copper nanoparticles; it is non-toxic, biocompatible, and antiseptic. The safety and antimicrobial pharmacodynamics of this medication were evaluated in periapical surgery. An experimental study—a Phase I clinical trial—was conducted on a sample of 36 patients with a clinical and radiographic diagnosis of chronic periapical disease requiring surgical treatment, who were treated at the Mexicali School of Dentistry, Autonomous University of Baja California, Mexico, from January 2022 to December 2025. All were healthy patients who underwent periapical surgery with topical application of the EPX® Biomolecule, in the form of a surgical gel, with the patients’ consent and under the multidisciplinary care of specialists in Oral and Maxillofacial Surgery and Endodontics. All patients had a favorable outcome, with signs and symptoms within normal parameters. Radiographic follow-up was favorable, with most patients showing signs of bone regeneration and no recurrent septic complications. No adverse reactions to the EPX® Biomolecule as an intraoperative gel were reported; doses were standardized in proportion to the size of the periapical lesion, and surgical wound healing was excellent in all patients, whether the procedure was simple or combined with bone grafting.