Regenerative endodontics is a developing field involving the restoration of tooth structure and re-vitality of necrotic pulp. One of the most critical clinical considerations for regenerative endodontic procedures is the disinfection of the root canal system, since infection interferes with regeneration, repair, and stem cell activity. In this study, we aimed to provide the synthesis of injectable biopolymeric tissue scaffolds that can be used in routine clinical and regenerative endodontic treatment procedures using Gelatin methacryloyl (GelMA), and to test the antimicrobial efficacy of Gelatin methacryloyl/Silver nanoparticles (GelMA/AgNP), Gelatin methacryloyl/Hyaluronic acid (GelMA/HYA), and Gelatin methacryloyl/hydroxyapatite (GelMA/HA) composite hydrogels against microorganisms that are often encountered in stubborn infections in endodontic microbiology. Injectable biocomposite hydrogels exhibiting effective antimicrobial activity and non-cytotoxic behavior were successfully synthesized. This is also promising for clinical applications of regenerative endodontic procedures with hydrogels, which are proposed based on the collected data. The GelMA hydrogel loaded with hyaluronic acid showed the highest efficacy against Enterococcus faecalis, one of the stubborn bacteria in the root canal. The GelMA hydrogel loaded with hydroxyapatite also showed a significant effect against Candida albicans, which is another bacteria responsible for stubborn infections in the root canal.