The objective of the study was to synthesis silica nanoparticles modified with (i) a tertiary amine bearing two t-cinnamaldehyde substituents or (ii) dimethyl-octyl ammonium, alongside the well-studied quaternary ammonium polyethyleneimine nanoparticles. These were to be evaluated for their chemical and mechanical properties, as well for antibacterial and antibiofilm activity. Samples were incorporated in commercial dental resin material and the degree of monomer conversion, mechanical strength, and water contact angle were tested to characterize the effect of the nanoparticles on resin material. Antibacterial activity was evaluated with the direct contact test and the biofilm inhibition test against Streptococcus mutans. Addition of cinnamaldehyde-modified particles preserved the degree of conversion and compressive strength of the base material and increased surface hydrophobicity. Quaternary ammonium functional groups led to a decrease in the degree of conversion and to low compressive strength, without altering the hydrophilic nature of the base material. In the direct contact test and the anti-biofilm test, the polyethyleneimine particles exhibited the strongest antibacterial effect. The cinnamaldehyde-modified particles displayed antibiofilm activity, silica particles with quaternary ammonium were ineffective. Immobilization of t-cinnamaldehyde onto a solid surface via amine linkers provided a better alternative to the well-known quaternary ammonium bactericides.