In vivo confocal microscopy (IVCM) findings of 84 patients who had undergone conventional epithelium-off corneal collagen crosslinking (CXL) and accelerated CXL (ACXL) were retrospectively reviewed. Analysis confirmed that despite a significant decrease in the mean density of anterior keratocytes in the first 6 postoperative months, cell density after CXL and ACXL returned to baseline values at 12 months. The demarcation lines observed after treatments represent an expression of light-scattering (reflectivity changes) through different tissue densities. Temporary haze of the anterior-mid stroma after conventional CXL represents an indirect sign of CXL-induced stromal collagen compaction and remodeling. IVCM showed that treatment penetration varies to some extent, but that the endothelium is not damaged and is correlated with CXL biomechanical effects. IVCM of limbal structures shows no evidence of pathological changes. Regeneration of subepithelial and stromal nerves was complete 12 months after the operation with fully restored corneal sensitivity and no neurodystrophic occurrences. IVCM allowed detailed high magnification in vivo micromorphological analysis of corneal layers, enabling the assessment of early and late corneal modifications induced by conventional and accelerated CXL. IVCM confirms that CXL is a safe procedure, which is still undergoing development and protocol adjustments.