Purpose: The purpose of this paper is to report the clinical manifestations, diagnostic evaluation, management and outcomes of microsporidial keratitis in post-keratoplasty eyes. Methods: This is a retrospective review of three patients diagnosed with microsporidial stromal keratitis in post-keratoplasty eyes between January 2012 and December 2021 at a tertiary referral center (Ospedali Privati Forlì “Villa Igea”, Forlì, Italy). Results: All patients presented with fine multifocal granular infiltrates following keratoplasty for a presumed herpetic keratitis. No microorganisms were isolated from the corneal scrapings and no clinical response was observed with broad-spectrum antimicrobial therapy. In all cases, confocal microscopy demonstrated spore-like structures. The histopathologic examination of the excised corneal buttons confirmed the diagnosis of microsporidial stromal keratitis. Following therapeutic keratoplasty and treatment with an initial high dose and extended taper of topical fumagillin, clinical resolution was achieved in all eyes. The Snellen visual acuities at the final follow-up were 20/50, 20/63 and 20/32. Conclusions: Prior to definitive surgery, confocal microscopy can be employed for the in vivo detection of pathogenic microorganisms such asMicrosporidium. In post-keratoplasty eyes, therapeutic keratoplasty and an initial high dose of topical fumagillin with extended taper can allow the resolution of microsporidial stromal keratitis with a satisfactory visual prognosis.