Objective: To evaluate the effect of enamel conditioning methods, that is, total-etch and rinse (TER), Er,Cr:YSGG (ECYL), and photodynamic therapy (PDT) on the shear bond strength (SBS) of orthodontic metallic brackets bonded using Zirconium oxide experimental adhesive (ZOEA). Methods: Sixty human incisor buccal surfaces were cleaned and allocated into three groups based on the method of enamel surface treatment, that is, TER using 37% phosphoric acid gel, methylene blue photosensitizer activated by PDT and ECYL (n = 20 each). Each group was further divided into two subgroups (n = 10) based on the type of adhesive, that is, ZOEA and experimental adhesive (EA). Metallic brackets were seated using composite resin. Samples were placed in a universal testing machine for SBS and failure mode using the ARI index. One-way analysis of variance and post hoc Tukey were used for multiple comparisons. ARI was presented in percentages in different investigated groups. Results: TER+ZOEA (17.16 ± 0.41 MPa) displayed the highest bond integrity. However, group PDT+EA (11.34 ± 0.25 MPa) demonstrated the lowest bond scores. The intergroup comparison revealed that the TER system displayed significantly higher SBS values than the PDT and ECYL groups (p < 0.05). The intragroup comparison revealed that enamel conditioned with TER and brackets bonded with ZOEA and EA displayed comparable bond integrity (p > 0.05). Conclusions: Enamel conditioned with TER bonded to a metallic bracket displayed better bond strength than PDT and ECYL. Zirconium oxide nanoparticles incorporated in adhesive have proved to be promising in improving the bond integrity of adhesive.