Background: We aim to evaluate the effect of surface conditioning, bonding agents and composite types on surface roughness (SR) and shear bond strength (SBS) of clear aligner composite attachments bonded to ceramics. Methods: One hundred and eighty IPS e.max CAD specimens were prepared. For SR, 60 specimens were divided according to surface conditioning (n = 15) into four groups: control, 9.6% hydrofluoric acid (HFA), 37% phosphoric acid (PhA), air abrasion (AA). SR was measured using a Profilometer and Atomic Force Microscopy. For SBS, 120 specimens were divided according to conditioning methods (n = 40) (9.6% HFA and 37% PhA or AA), then according to bonding agents (n = 20) (Assure universal bond (AUB) or Single bond universal (SBU)) and then according to composite type (n = 10): Filtek™ Z350 and Filtek™ Z350 XT flowable composite. SBS was measured using Instron testing machine. Descriptive and group comparison were calculated (p < 0.05). Results: AA had the highest SR, while the control had the lowest SR (p < 0.05). HFA had the highest, but insignificant SBS, followed by AA (p > 0.05). AUB had higher SBS than SBU (p < 0.001). Filtek™ Z350 produced higher SBS than Filtek™ Z350 XT flowable composite (p < 0.01). Conclusion: The combination of AA, AUB, and Filtek Z350 produced the highest SBS, followed by HFA, AUB, and Filtek Z350.