Kinga Mária Jánosi, Diana Cerghizan, Izabella Éva Mureșan, Aurița Ioana Albu, Liana Claudia Dobreci, Liana Georgiana Hănțoiu, Alpár Kovács, Sharukh S Khajotia, Cristina Nicoleta Ciurea
Background: Dentin disinfection plays an important role in prosthodontics, reducing the microbial load, preventing postoperative complications and enhancing the bond strength. This in vitro study aims to evaluate the antimicrobial efficacy of different dentin disinfection protocols, depending on microorganism type, application time, and dentin depth. Methods: A total of 144 extracted human molars were included in the final analysis. The exposed dentin surfaces were contaminated with methicillin-resistant Staphylococcus aureus (MRSA) or Candida albicans (C. albicans). The specimens were disinfected using 2% chlorhexidine digluconate, 3% hydrogen peroxide, or photodynamic therapy with 1% toluidine blue. Microbial growth at superficial and deep dentin was assessed using semi-quantitative visual colony-density scores, resulting in 288 microbiological measurements. Ordinal generalized estimating equation (GEE) models, accounting for within-tooth correlation, were used to evaluate the factors associated with microbial scores. Results: The results showed statistically significant differences among protocols for MRSA (Wald χ2 = 62.98; df = 5; p < 0.001) and for C. albicans (Wald χ2 = 18.77; df = 5; p = 0.002). Specifically, 2% CHX applied for 30 s was associated with the greatest reduction in MRSA microbial scores (OR = 0.121; p = 0.009), whereas 3% H2O2 applied for 60 s was more effective against C. albicans (OR = 0.054; p < 0.001). PDT showed lower and less consistent antimicrobial effects under the tested parameters. Conclusions: The effectiveness of dentin disinfection depends on the microorganism, application time, and dentin depth. Complete elimination of the microbial load cannot be achieved using the disinfectants investigated.