Background Enamel etching is of utmost importance during the orthodontic bonding procedure. Phosphoric acid, hydrofluoric acid, and citric acid are used in specific concentrations to create surface irregularities on enamel surfaces, enhancing the bond strength of the orthodontic attachment. Therefore, it is essential to evaluate the type of etchant for reliable orthodontic bracket bonding with minimal damage to the enamel surface. Aims and objectives This study aimed to investigate the morphological changes on the enamel surface after treatment with different surface etchants, assess the depth of penetration, and evaluate the shear bond strength (SBS) of orthodontic brackets. Materials and methods One hundred and one extracted premolar teeth were used to investigate morphological changes on the enamel surface treated with 37% phosphoric acid, 11% hydrofluoric acid, and 20% citric acid. It was evaluated on a scanning electron microscope (Jeol Scientific Equipment, Jeol Limited, Akishima, Japan), and the SBS of brackets on enamel treated with different etching agents was evaluated using an Instron Universal Testing Machine (UTM; Instron Model: 5982, Universal Testing Systems, Norwood, MA). Group A had 60 test samples. Group B had 40 test samples. One control without any acid etching was used in both groups. Subgroup A1 (n = 30) was evaluated for surface characteristics of acid-etched enamel. Subgroup A2 was assessed for the penetration depth of various etchants. Group B (n = 40) was tested for SBS. The results were tabulated and analyzed using IBM SPSS Statistics, version 20.0 (IBM Corp., Armonk, NY). Post hoc Tukey HSD test and one-way analysis of variance were used to assess SBS and penetration depth of etchants (P ≤ 0.05). Pearson's correlation test was used to correlate SBS, etching pattern, and penetration depth. The chi-square test was used to test the frequency of types of etching patterns. Results Intergroup correlations between etching depth, etching pattern evaluated on SEM, and SBS evaluated on the UTM showed a high statistical correlation between etching depth & SBS, etching depth & etching pattern, and SBS & etching pattern between A1, A2, and group B (P ≤ 0.001). A highly significant negative correlation between SBS & etching pattern (P = 0.42) was observed among intra-group correlation. Non-significant correlations were found between etching depth & SBS and etching depth & etching pattern within the 20% citric acid etch group (P = 0.370 and 0.141, respectively). Conclusion Penetration depth obtained was highest with 11% hydrofluoric acid, followed by 37% phosphoric acid and20% citric acid. In addition, 11% hydrofluoric acid showed the highest bond strength. Acid etching showed better penetration depth and bond strength than control.