The aim of this study is to develop a novel 3D printed denture base resin material modified with mesoporous silica nanocarrier loaded with silver (Ag/MSN) to enhance mechanical and antimicrobial properties. Acrylate resin-based was incorporated with various proportion of Ag/MSN (0.0–2.0 wt%). Specimens with different geometry were printed and characterized accordingly for the effect of modification on properties such as: mechanical and physical properties, chemical composition and degree of conversion, as well as biological response in term of biocompatibility and antimicrobial against oral fibroblast and candida biofilm (C. albicans), respectively. The consecutive addition of Ag/MSN improved significantly surface hardness and crack propagation resistance, while flexural strength remained similar to control; however, a negligible decrease was observed with higher concentrations ≥1 wt%. No significant difference was noticed with water sorption, while water solubility had a remarkable trend of reduction associated with filler content. The surface roughness significantly increased when concentration of Ag/MSN was ≥1.0 wt%. A significant reduction in C. albicans biofilm mass, as the inhibition proficiency was correlated with the proportion of the filler. With respect to the amount of Ag/MSN, the modification was compatible toward fibroblast cells. The sequential addition of Ag/MSN enhanced significantly the mechanical and antimicrobial properties of the 3D printed resin-based material without affecting adversely compatibility. The acrylic resin denture base material has susceptibility of microbial adhesion which limits its application. Silver loaded MSN showed a significant performance to enhance antimicrobial activity against C. albicans which is the main cause of denture stomatitis. The proposed invention is a promise technique for clinical application to provide an advanced prosthesis fabrication and serve as long-term drug delivery.