The aim of this study was to compare one-visit indirect pulp treatment (IPT), two-visit IPT, and direct complete excavation (DCE) of deciduous and young permanent molars with deep carious lesions from clinical and microbiological points of view. One hundred thirty-five teeth (83 deciduous molars and 52 young permanent molars) were included in the study. The teeth were randomly selected and treated either with one-visit IPT, two-visit IPT, or DCE. For two-visit IPT, the final excavation was performed after a period of 3 months. The color, consistency, and humidity of the dentin at the cavity floor were recorded for clinical assessment, and dentin samples were obtained from all teeth. Dentin samples were microbiologically investigated for the total number of colony forming units, mutans streptococci, and lactobacilli. The results showed bacterial growth in 63.8% of the dentin samples in one-visit IPT, while in two-visit IPT, bacterial growth was observed in all of the samples (100%) after the first excavation. When the cavities were reopened before the final excavation, the number of samples with positive growth had decreased significantly (44.4%), and after the final excavation, the number of the samples with positive growth had decreased to 2.2%. In the DCE group, only 25.6% of the samples revealed bacterial growth. No statistical difference was found between deciduous and permanent molars in any of the treatment groups in terms of microbiologic results (p > 0.05). In conclusion, although none of the treatment methods completely eliminated the viable microorganisms during the initial excavations, a dramatic reduction in bacterial growth was detected during the treatment stages of two-visit IPT.