Objective <p>The aim of the present study was to evaluate the effect of photodynamic therapy on the reduction of bacteria in deep carious lesions of primary teeth.</p> Materials and methods <p>Thirty-six children presenting with deep carious lesions in primary molars were included in this randomized clinical study. After selective caries excavation, dentin samples were collected. Participants were randomly assigned to two groups according to the photosensitizer applied: 0.1% toluidine blue gel (FotoSan Agent^® High) or curcumin QroxB2^®. In both groups, aPDT was performed using the same diode lamp (FotoSan^® 630; 630&#xa0;nm) to ensure standardized clinical conditions. Dentin samples were collected before and after aPDT. Microbiological analysis was performed using conventional culture methods, and colony-forming units (CFU/ml) were quantified. Strain identification was performed using the VITEK^® MS system (bioMérieux SSC, France).</p> Results <p>A statistically significant reduction in the total number of microorganisms was noted after therapy. A decrease in bacterial counts was also observed on selective media for total <i>Streptococci</i> and <i>Streptococcus mutans</i>. The degree of microbial reduction did not significantly differ depending on the photosensitizer used.</p> Conclusions <p>Within the limitations of this study, antimicrobial photodynamic therapy significantly reduced bacterial counts in deep carious lesions of primary teeth and may serve as an adjunctive method in selective caries excavation.</p> Clinical Significance <p>Photodynamic therapy may be used as an adjunct in selective caries excavation.</p>