This work evaluated the efficacy of an improved method used to determine the frequency of bacterial infiltration and bacterial population levels and morphotypes in cavities restored with adhesive composites in conventional mice. By using the alternative methodology suggested in this work, bacteria from microleakage were recovered and identified in cavities subjected to restoration procedures that used acid etching of the dentin and dentin adhesives used with light-curing resin. The methodology presented herein seems to be more effective than the one normally used to investigate the presence of bacteria, which uses acid demineralization of dental structures for the histological processing of tissues. The results suggest that the methodology presented in this work made it possible to recover and identify Gram-negative and Gram-positive bacteria from microleakage. Frequencies of microleakage and bacterial population levels in restored cavities using two different adhesive systems were not statistically different (p < 0.05).