Presurgical infant's orthopedic appliances (PSIOs) play an increasingly crucial role in the interdisciplinary management of neonatal CLP, aiming to improve and maintain adequate nasolabial aesthetics, followed by primary lip/nasal surgery in both unilateral and bilateral CLP cases. The use of PSIOs in cleft lip and palate patients can lead to contamination with oral microflora, acting as a potential reservoir for infectious microorganisms. Acrylic surfaces might provide retention niches for microorganisms to adhere, and inhabit, which is difficult to control in immunocompromised patients, thus predisposing them to increased infection risks. The objective of this multi-assay in vitro study was to investigate the effects of incorporating chlorhexidine-loaded halloysite nanotubes (CHX-HNTs) fillers on the morphological, cytotoxic, release, and antimicrobial characteristics of self-cured acrylic polymethyl methacrylate (PMMA) material used in pre-surgical orthopedic appliances. Disk-shaped PMMA specimens were prepared with varying proportions of CHX-HNTs. A control group without any addition served as a reference, and four experimental samples contained a range of different concentrations of CHX-HNTs (1.0, 1.5, 3, and 4.5 wt%). The antimicrobial efficacy was assessed using an agar diffusion test against common reference microorganisms: Candida albicans, Staphylococcus aureus, Streptococcus pneumoniae, and Streptococcus agalactiae. Cytotoxicity was examined using the L929 cell line (mouse fibroblasts) through a (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide, MTT) cell viability assay. The release kinetics of CHX were monitored using UV-spectral measurements. The statistical analysis used a one-way ANOVA followed by Tukey's post hoc test. The integration of CHX-HNTs in PMMA exhibited a substantial dose-dependent antifungal and antibacterial effect against microorganisms at tested mass fractions (1.0 to 4.5 wt%). CHX release was sustained for up to 60 days, supporting prolonged antimicrobial activity. Furthermore, no significant cytotoxicity was determined in the L929 fibroblast cell line (control), indicating the biocompatibility of the CHX-HNTs-enhanced PMMA. Incorporating CHX-HNTs in PMMA successfully enhanced its antimicrobial properties, providing sustained CHX release and superior antimicrobial efficacy. These findings demonstrate the potential of antimicrobial nanoparticles in dental therapies to improve therapeutic outcomes. However, rigorous further clinical trials and observational studies are warranted to validate the practical application, safety, and efficacy. This study has the potential to make a major impact on the health of infants born with cleft lip and palate by helping to reduce the prevalence of infectious illnesses. The incorporation of CHX-HNTs into PMMA-based appliances is a novel promising preventive approach to reduce microbial infections.