Background: The purpose of this study was to identify differences in clinical corneal findings after standard and accelerated epithelial off cross-linking (CXL) during a long-term follow-up. Methods: Two hundred forty-one patients (184 male) were included in this monocentric, retrospective, non-randomized and unmasked study. One hundred forty-eight eyes were treated with the accelerated protocol and 138 with the standard protocol with epithelial off CXL, if diagnosed with keratoconus and a progression in Kmax of more than one dioptre during the preceding 6 months, plus a minimal pachymetry measurement of 400 mu m in keratometry (Pentacam, Oculus GmbH, Wetzlar, Germany). Exclusion criteria were previous surgery, other corneal conditions or age above 50 years. Follow-up time was 36 months with clinical examination and keratometry at every visit. Outcome measures were the observed rate of corneal changes, differences between treatment groups and correlation with keratometry measurements. Results: In patients with accelerated CXL, significantly more clear corneas were seen at three (p = 0.015) and six (p = 0.002) months after surgery than following the standard protocol. The rate of clear corneas dropped from 52.2% pre-operation (OP) to a minimum of 19.3% after 6 months in the standard protocol group compared with 50.7% clear corneas pre-OP and a minimum of 40.8% in the accelerated group. In the standard protocol group, more striae were found 3 months after intervention than in the accelerated group (p = 0.05). Conclusions: In patients with accelerated CXL, fewer morphological corneal changes were observed than after conventional CXL. However, rarely, corneal changes persisted for a long time.