The present study aimed to evaluate the influence of application mode on the short-term microshear bond strength longevity of self-etching and universal adhesive systems to enamel, the failure mode, and the resulting enamel surface micromorphology. Ninety enamel surfaces were obtained from sound third molars, planed, and randomly assigned to nine groups, according to the application mode and the adhesive system (n=10). There were three primer application modes: according to the manufacturer's recommended application time (control), using double the application time recommended for the primer and selective enamel etching. The adhesive systems used were: Clearfil SE Bond (Kuraray), FL-Bond II (SHOFU), and Futurabond U (Voco). At least two resin-bonded composite cylinders (Grandioso Light Flow, Voco) were placed on each enamel surface, and then evaluated for microshear bond strength at 24 hours and 180 days of storage in solution body fluid (SBF) at pH 7.4. Failure modes were evaluated with a stereoscopic microscope at 20× magnification. A micromorphological analysis of the enamel surface was performed under a scanning electron microscope at 5000× magnification before and after the treatments. Mixed models for repeated measures over time showed significant interaction among application modes, adhesive systems, and time periods (p=0.0331). The bond strength of FL-Bond II adhesive to enamel observed after performing selective enamel etching was significantly higher than that observed after applying the control treatment (p=0.0010) at both 24 hours and 180 days. However, no significant difference was observed between the application of this same adhesive at double the time recommended by the manufacturer and the other two application modes (p>0.05). There was also no significant difference in the microshear bond strength for the enamel treatments applied using Clearfil SE Bond and Futurabond U (p>0.05). A significant reduction in bond strength to enamel was observed at the 180-day storage time for all the adhesive systems when selective enamel etching was performed (p<0.0001). No significant association was observed between the adhesive system failure mode and the enamel treatments (p=0.1402 and p=0.7590 for 24 hours and 180 days, respectively). The most prevalent failure was the adhesive type.