The relationship between clinical characteristics of carious dentin and bacterial colonization after partial caries removal is not completely understood. The aim of this study was to compare microbial counts between categories of carious dentin color, consistency and humidity, and to evaluate the correlation between these characteristics and the presence of cariogenic microorganisms in deep cavities (2/3 or more of the dentin thickness) submitted to partial caries removal. Sixteen primary teeth were submitted to the removal of all carious tissue from the lateral walls of the cavity, whereas carious tissue of the pulp wall was removed superficially. Dentin in the pulp wall was classified according to color, consistency and humidity immediately after cavity preparation and 3–6 months after cavity sealing and a tissue sample was collected on the same occasion for microbiological evaluation. Before sealing, Streptococcus mutans (p = 0.033) and Lactobacillus spp. (p = 0.048) counts were higher in cavities with humid dentin compared to cavities with dry dentin. A negative correlation was observed between carious dentin consistency and S. mutans count during this phase (r_s = –0.571; p = 0.020). Arrest of dentinal caries lesions was observed after sealing, which was characterized by a reduction of bacterial counts and changes in dentin color, consistency and humidity, irrespectively of baseline dentin characteristics. The clinical characteristics of carious dentin change after the period of cavity sealing and cannot be applied as absolute indicators to limit the excavation of carious dentin when minimally invasive techniques are used.