Purpose: This in vitro study aimed to evaluate and compare the physical and antimicrobial properties of provisional resin modified with two different nanoparticles, namely, silicon dioxide (nano-SiO2) and titanium dioxide (nano-TiO2). Methods: A commonly used commercially available polymethyl methacrylate (PMMA) provisional resin (Unifast III; GC Corp) was modified with nano-SiO2 and nano-TiO2 at different concentrations (1% wt. and 2.5% wt. respectively), while one unmodified group was used as a control. Rectangular specimens (60 × 10 × 3.3 mm) for strength (MPa) and elastic modulus, and square specimens (10 × 10 × 3.4 mm) for surface roughness (Ra, µm), hardness (VHN), and Candida albicans adhesion (colony forming unit, CFU/mL) were prepared and grouped into five groups (n = 10) according to (nanoparticles) NPs type and concentration. After polymerization, the specimens were finished and polished and then subjected to thermal cycling (5000 cycles). Analysis of variance and post-hoc Tukey test were used for data analysis (α = 0.05). The scanning electron microscope (SEM) was used for fracture surface analysis and C. albicans count. Results: The addition of 1% nano-SiO2 significantly increased the flexural strength, and 1% nano-SiO2 contributed to the highest flexural strength value, while 2.5% nano-SiO2 and nano-TiO2 showed non-significant increases (p > 0.05). The elastic modulus increased significantly for both NPs. Among the NP-modified groups, the nano-SiO2 groups showed an increased elastic modulus compared to the nano-TiO2 groups. The hardness significantly increased with NPs addition with no significant differences between NPs-modified groups. Surface roughness increased with 2.5% nano-TiO2 addition, while 1% nano-TiO2 and nano-SiO2 showed non-significant differences. Nano-SiO2 and nano-TiO2 significantly decreased C. albicans adhesion, and nano-TiO2 groups were significantly superior in their antimicrobial effect compared with nano-SiO2. Conclusions: Low nano-SiO2 addition increased the flexural strength of provisional resin. The addition of NPs increased elastic modulus and hardness and decreased the C. albicans adhesion to provisional resin. Nano-SiO2 did not alter the surface roughness, while 2.5% of nano-TiO2 increased the surface roughness.