The incorporation of antimicrobial agents into 3D-printed resins may improve their biological performance; however, their effects on physicochemical and mechanical properties remain unclear. This study evaluated the influence of phosphorylated chitosan (P-Chi; 0.25% and 0.50% w/w) incorporated into short- (ST) and long-term (LT) 3D-printed dental resins. Surface, mechanical, optical, and antibacterial properties against Streptococcus mutans were investigated using standardized methods. FTIR confirmed the successful phosphorylation and incorporation of P-Chi into both resin matrices. P-Chi significantly reduced S. mutans CFU counts compared with the control (p < 0.001, η²p = 0.286), regardless of concentration, although no inhibition halos were detected, indicating a contact-dependent antimicrobial mechanism. Enhanced antibacterial activity was accompanied by increased surface roughness and wettability. Nanoparticle concentration significantly affected mechanical performance (p = 0.001), whereas resin type did not (p = 0.613). The 0.25% groups exhibited lower flexural strength and microhardness than the controls (p < 0.05), while the 0.50% groups maintained flexural strength comparable to that of the controls, with G6 showing the highest elastic modulus (3494.95 ± 301.30 MPa). Color variation was influenced by resin type rather than P-Chi concentration (p < 0.05). Overall, P-Chi enhanced antibacterial activity while maintaining clinically acceptable mechanical properties, supporting its use as a multifunctional additive for biofunctional 3D-printed provisional resins.