Numerous failures in root canal treatment (RCT), attributed to the persistence of adverse microbiota, prompted researchers to develop a biomaterial with effective antibacterial and antifungal properties. In our systematic review, emphasis was placed on examining the antimicrobial properties of gutta-percha, the most used material for root canal obturation. The review aimed to determine whether gutta-percha demonstrated adequate antibacterial and antifungal features. Additionally, it sought to identify specific substances added to gutta-percha’s composition that could enhance the success rate of root canal obturation. On October 30, 2023, electronic searches were systematically performed in the PubMed, Web of Science (WoS), and Scopus databases using the specified keywords: ((antibacterial) OR (antimicrobial)) AND ((gutta-percha) OR guttapercha)). A thorough evaluation commenced, with an initial pool of 330 studies, from which 174 duplicates were methodically identified and removed. The ultimate dataset for qualitative synthesis consisted of 26 studies. The results of the compared studies did not unequivocally indicate whether the use of gutta-percha alone exhibits antibacterial or antifungal effects. Among the six studies demonstrating results supporting gutta-percha’s antimicrobial activity, five showed activity against Enterococcus faecalis. Conversely, six studies concluded that gutta-percha lacks any discernible antimicrobial features. One study even suggested that gutta-percha might promote the progression of bacterial development. However, eight out of nine studies demonstrated an increase in gutta-percha’s antimicrobial properties after the addition of chlorhexidine. Furthermore, calcium hydroxide and iodoform also improved gutta-percha’s properties, showing promising results. Unfortunately, none of the materials added to gutta-percha displayed comprehensive improvement in its antimicrobial efficacy, including activity against Enterococcus faecalis. The review demonstrated the benefit of enhancing gutta-percha with chlorhexidine, calcium hydroxide, and iodoform. Nevertheless, achieving the inactivation of Enterococcus faecalis posed a challenge.