Minimally invasive treatment protocols may leave a residual layer of carious dentin, which requires treatment for the inhibition of bacterial growth beneath restorations. We aimed to examine the in vivo effect of silver diammine fluoride (SDF) and SDF + potassium iodide (KI) application on bacteria present in deep carious lesions. We studied the in vivo efficacy in five patients, each of which had five carious lesions. Dentin samples taken before and after treatment were subjected to microbial analyses. Following treatment with SDF, the median colonyforming unit (CFU) counts per mg of dentin reduced from 9 × 10 5 to 1.6 × 10 2 (P <0.05), and following that with SDF + KI, the counts decreased from 2.9 × 10 5 to 9.2 × 10 (P <0.05). The use of chlorhexidine gluconate (CHX) reduced CFU counts from 1.1 × 105 to 4.8 × 10 2 (P <0.05). In four of the five patients, no CFUs were found on mitis salivarius-bacitracin agar with respect to SDF or SDF + KI application. For CHX, the median CFU count before treatment was 1.6 × 10 3 and that after treatment was 1.1 × 10 2 . SDF completely inhibited mutans streptococci growth in four of the five patients, while the growth of anaerobes was not completely inhibited.