The aim of the study was the morphological analysis of coronal dentin caries and the modifications induced by different pretreatments with phosphoric acid or sodium hypochlorite. Carious dentin specimens were obtained from human molars affected by carious lesions. Specimens were divided in four groups and submitted to: (1) untreated; (2) 35% phosphoric acid for 15 s; (3) 35% phosphoric acid for 15 s and 5% sodium hypochlorite for 2 min; (4) sodium hypochlorite for 5 min. Specimens were observed under high-resolution SEM. Different areas were identified within the carious lesion: a deeper, inner region revealing closed highly mineralized tubules, and a more superficial outer layer showing an increasing demineralization rate toward the surface of the lesion. Phosphoric acid followed by NaOCl treatment removed all collagen fibrils from greatly altered carious outer-dentin layer. The 5-min treatment with sodium hypochlorite affected both inner and outer dentin, removing all collagen fibrils and increasing the porosities of deeper intertubular hypermineralized dentin. FEISEM analysis confirmed that only inner carious dentin after phosphoric acid treatment may be considered a suitable substrate for dentinal bonding system. On the contrary, the outer dentin is an unstable substrate for any type of bonding systems and must be avoided/removed from any surface before conditioner application.