Objective To evaluate the inhibition zone formation (IZ) and mineral distribution along the interface of adhesive systems either containing fluoride and antibacterial primer or not, after chemical and biological artificial caries challenges. Methods Forty-eight third molars were used. Artificial caries was developed with S. mutans in a 4 mm × 4 mm area of occlusal dentin surface. Carious dentin was removed and cavities were restored with Adper Scotchbond Multi-Purpose (SBM) and Clearfil Protect Bond (CPB) ( n = 24). Samples were submitted to secondary caries development by chemical (C) (acidic gel) or biological (B) ( S. mutans culture) methods for 5 days. Four groups were tested ( n = 12): (1) SC (SBM + C); (2) SB (SBM + B); (3) CC (CPB + C); (4) CB (CPB + B). The IZ and outer lesion (OL) formations were analyzed by confocal laser scanning microscopy (CLSM). The distribution of calcium (Ca) and phosphorus (P) content along the interface was analyzed by micro X-ray fluorescence spectrometer by energy-dispersive (μEDX). Results The frequency of IZ formation and mean values of IZ thickness differed among the groups. The CC group presented the lowest OL depth. μEDX analysis showed that CPB had the highest mineral loss by the biological method, but the lowest mineral loss by the chemical method. SC and SB groups showed intermediate values of mineral loss. Conclusion The mineral loss along the dentin/restoration interface was affected by the artificial caries method, and hybrid layer formation by adhesive systems used. The adhesive system containing fluoride and antibacterial primer did not prevent secondary caries formation.