Although acid-etching could increase enamel bond strength of self-adhesive (SA) cements, it may lead to negative effect on dentin. The aim of this study was to assess the effect of shortening of phosphoric acid pre-etching duration on enamel/ dentin shear bond strength (SBS) and interfacial microstructure of Panavia SA Luting Plus (PASA) and Bifix SE (BXSE). For both enamel and dentin, effect of pre-etching time was significant (p<0.001); however, effect of cement brand and the interaction of two factors was significant only for dentin (p?0.008). Three pre-etching times increased SBS of both cements to enamel and BXSE to dentin. In case of dentin SBS of PASA, this improvement was significant only for 5 and 10 seconds (p<0.001). Adding acid-etching in the three times to both cements similarly improved interfacial adaptation, particularly for enamel. The evaluations of the biofilm elimination showed results that indicate that the 4% sodium hypochlorite group with positive pressure irrigation presented significant differences with the group that had irrigation with sodium hypochlorite activated with XP-endo Finisher and the chlorhexidine groups to 2% (P<0.05). Interfacial bond strength and adaptation of SA cements used in this study were improved following addition of enamel/dentin etching step for a short time. This was not exceeded for longer times than 5-second.