Objective: This systematic review aimed to evaluate material-based modifications of resorbable root canal filling materials for primary teeth, assessing how compositional changes—including bioactive additives, antimicrobial agents, and alternative base matrices—influence antimicrobial performance. Methods: A systematic search of PubMed, Scopus, Web of Science (WoS), and Embase was performed in October 2025. Search terms included (primary teeth OR deciduous teeth) AND (root canal filling materials OR root canal filling OR canal obturation) AND (antibacterial agents OR antibacterial OR antimicrobial). Study selection adhered to PRISMA 2020 standards and was systematically organized through the PICO framework. From 199 identified records, 18 studies met the eligibility criteria. Results: Most studies evaluated modified zinc oxide-based materials. Additives such as propolis, Morinda citrifolia extract, Aloe vera, and olive oil enhanced antimicrobial activity or improved clinical and radiographic outcomes compared with conventional zinc oxide–eugenol. Triclosan-containing formulations consistently demonstrated strong antibacterial effects. In contrast, chlorhexidine yielded variable results, with some calcium hydroxide–based pastes showing superior performance in its absence. Antibiotic-enriched materials exhibited high antimicrobial efficacy; however, several studies raised concerns regarding the potential development of bacterial resistance. Conclusions: Most of the introduced modifications of resorbable root canal filling materials for primary teeth enhance antimicrobial activity and their physicochemical properties in vitro. Clinical evidence is limited and heterogeneous, and therefore, its superiority over conventional materials cannot be definitively determined. Further long-term, randomized clinical trials on large patient groups, evaluating the same modifications, are needed to confirm the effects observed in laboratory studies.