In this study, some physicochemical and antibacterial properties of three root canal filling materials for primary teeth, Calplus “CP” (Prevest DenPro, Lewes, DE, USA), Bio-C Pulpecto “Bio-CP” (Angelus, Basil, Londrina, Paraná, Brazil), and Zinc Oxide and Eugenol “ZOE” (Prevest DenPro, Lewes, DE, USA) were compared. For each material, the pH, solubility, contact angle, and crystalline microstructure under SEM were evaluated. Their antibacterial activity against Enterococcus faecalis was determined through direct tests. The Kruskal–Wallis test was used to analyze the results using a one-way analysis of variance on ranks. All the materials had an alkaline pH at 3, 24, and 72 h, with CalPlus having the highest (p < 0.05). Bio-CP was more soluble during the evaluation period (24 h) than ZOE and CalPlus (p < 0.05). Bio-CP and ZOE demonstrated the creation of crystallite structures on their surfaces after immersion in PBS at 37 °C, whereas CalPlus showed none. The lowest contact angle was observed for Bio-CP (53 ± 1.5°); contact angles of (86 ± 4°) and (96 ± 1°), respectively, were observed after 10 s of the deposition of the water drop for CalPlus and ZOE. In conclusion, according to this study, there is still a need to develop new filling materials for primary teeth. ZOE, CalPlus and Bio-CP demonstrated different physicochemical and antibacterial properties, but none of the materials had optimal properties and could be considered the most suitable filling material for primary teeth pulpectomy. Bioceramics in their current state are not an alternative. The physicochemical and antibacterial properties still need improvement to fit the intricate anatomy of primary teeth.