This study compared the shear bond strength (SBS) and micromorphology of composite resin to human dentin after pre-treatment with silica-modified aluminum oxide air abrasion. Forty-six molar teeth were treated with either Scotchbond Multi-Purpose (SCMP) or Clearfil SE Bond (CLSE) adhesive. Buccal surfaces were pre-treated with the CoJet air abrasion system (SB), and lingual surfaces were controls. The adhesion of light-cured resin composite to the treated dentin surface was evaluated with SBS. After debonding, substrate surfaces were examined with an optical microscope for failure analysis. In addition, 15 molar teeth were sectioned and randomly assigned to one of five groups, according to the dentin surface pre-treatment and adhesive type, and examined with high-vacuum scanning electron microscopy/energy dispersive X-rays (SEM/EDS). The type of adhesive had a significant effect on SBS (p = 0.000); CLSE had the highest values. SB did not affect SBS (p = 0.090). SEM/EDS revealed residual aluminum and/or silicon on all dentin surfaces after SB, except for the control. Treatment with 32% phosphoric acid in the SCMP adhesive decreased the amounts of aluminum and silicon compared to SB dentin only, whereas CLSE resulted in similar quantities of aluminum and silicon as air-abraded dentin. The results of this study indicate that CLSE might have a higher bond strength to dentin than SCMP. Pre-treatment with SB does not appear to affect bonding strength.