Objective This study investigates the antimicrobial properties of silver (1%) and chitosan (1%) nanoparticles against Streptococcus mutans (S. mutans) when added to an orthodontic primer used for aligner attachments. While aligner treatments are becoming increasingly popular for their aesthetics and convenience, their attachments can create retention sites for bacteria, potentially leading to white spot lesions (WSLs). This in vitro study aims to address this issue by enhancing the antimicrobial efficacy of aligner primers. Methodology Thirty freshly extracted teeth were classified into the following three groups: Group A with the standard primer, Group B with chitosan nanoparticles mixed in the primer, and Group C with silver nanoparticles mixed in the primer. The samples were incubated with S. mutans and bacterial colonies were counted at 12, 24, 48, and 72 hours. Results The results showed a significant reduction in colony-forming units (CFUs) in the groups with nanoparticles compared to the control group, with silver nanoparticles exhibiting a higher antimicrobial effect than chitosan. Conclusions This study suggests that incorporating silver nanoparticles into orthodontic primers can effectively reduce bacterial growth, potentially improving oral hygiene and reducing the risk of WSLs in patients undergoing aligner treatment.