Aim of this study was to analyze Shear Bond Strength (SBS) and Adhesive Remnant Index (ARI) of ceramic and metallic orthodontic brackets bonded to zirconia or lithium-disilicate ceramics used for prosthetic restorations, conditioned with hydrofluoric acid (HFA) or phosphoric acid (PhA), as well as to determine the Porcelain Fracture Index (PFI), in order to examine the condition of the ceramic surface after debonding. Material and methods The research was conducted on 96 prepared all-ceramic samples divided into 8 groups combined from the type of ceramic material, orthodontic brackets, and surface conditioning. SBS was tested with Universal Testing Machine, and the samples were analyzed using a Scanning Electron Microscope, to determine ARI and PFI. Statistical data were processed using ANOVA, with the level of significance α = 0.05. Results Lithium-disilicate showed better bond strength in almost all groups. However, no significant difference between the groups was noticed and none of the factors had a significant influence on the mean values of SBS (p>0.05). Nevertheless, ARI significantly depended on the type of bracket (p = 0.005), and PFI significantly depended on the type of etchant (p = 0.029). Conclusion The use of HFA for surface etching of zirconia and lithium-disilicate, does not cause a significant increase in the SBS values as compared to etching with PhA and silane application. Furthermore, HFA can weaken the surface structure of the ceramic, and considering its toxicity, might not be the best suitable conditioner prior to orthodontic bonding to lithium disilicate, and in particular to zirconia, also taking into account its crystalline structure.