Keratoconus is an ectatic disorder that is presently considered one of the most prevalent reasons for keratoplasty. Corneal collagen crosslinking (CXL) is the only proven treatment option available that is capable of halting the progression of the disease by stabilizing the cone in 90% of cases, and by also reducing refractive error and maximal keratometry. This study assesses, by means of a 3D morphogeometric analysis procedure developed by our research team, the corneal structure changes that occur immediately after CXL treatment and during a 6 month follow-up period. A total of 19 eyes from 19 patients diagnosed with keratoconus who underwent CXL were included, and several variables derived from the morphogeometric analysis were calculated and evaluated for the pre-operative, 3 month postoperative, and 6 month postoperative states. Significant reductions were detected in central corneal thickness and corneal spherical-like root mean square (RMS) 3 months after surgery, with non-significant regression of the effect afterward. Significant reductions in the total corneal area/volume were found, with some levels of regression after 6 months in certain volumetric parameters. In conclusion, the eyes with higher values for morphogeometric parameters—posterior apex deviation (PAD), anterior minimum thickness point deviation (AMTPD), and posterior minimum thickness point deviation (PMTPD)—seemed more likely to undergo aberrometric improvement as a result of CXL surgery.