Almost 50 % of the U.S. population suffers from oral infections such as periodontitis. Current treatment options for periodontitis include mechanical cleaning procedures, which are performed often under local anesthesia and are time-consuming. Alternate option includes systemic antibiotics which increase the risk of antimicrobial resistance and are not recommended for prolonged usage. Topical treatments of gingiva-based antimicrobial agents have shown limited efficacy due to poor penetration of the therapeutic into deep gingiva where the infection resides. Herein, we report an Iongel of a Deep Eutectic Antimicrobial (IDEA), which simultaneously exhibits deep tissue penetration and antimicrobial activity against P. gingivalis. In vivo studies confirmed that IDEA successfully penetrated into the gingiva and the gingival sulcus, where the pathogens primarily exist, within a short time. In vitro studies confirmed that the dose delivered was adequate to inactivate P. gingivalis biofilm. In vivo studies in a periodontal rat model confirmed that a topical treatment of IDEA eliminated pathogenic bacteria, and the disease progression was significantly suppressed. Safety studies confirmed excellent tolerance to IDEA. Altogether, IDEA offers a promising topical agent against periodontitis.