The purpose of this study was to evaluate the histopathological factors in non-resolving cases of microsporidia stromal keratitis (MSK) through the study of corneal buttons obtained during therapeutic penetrating keratoplasty (TPK). This was a retrospective noncomparative consecutive case series. This case series included 22 corneal buttons (22 patients) of histologically diagnosed MSK between June 2015 and April 2023. Records of preoperative clinical and microbiological data, and postoperative microbiological and histopathologic data of the corneal buttons were evaluated. Histologic evaluation was conducted of the buttons for morphologic changes, degree and distribution of inflammatory cells, presence of microsporidial spores, and their degree and distribution within the corneal buttons. This study evaluated 22 patients with MSK, highlighting clinical, microbiological, treatment, and histopathological findings. The mean patient age was 57.1 ± 13.4 years (range = 22-83 years). The median interval from symptom onset to presentation was 4 months, and the mean time from presentation to keratoplasty was 1 month. Microsporidia spores were detected in 59% of cases through smears, with 41% of cases showing no organisms on microbiological tests. Targeted therapy using polyhexamethylene biguanide (PHMB) 0.02% was given in 13 cases, whereas 9 cases were treated empirically. Histopathology showed no significant correlation between the distribution of inflammatory cells and that of microsporidia. Moderate microsporidia severity correlated with longer symptom duration (10.0 ± 6.36 months). These findings underscore the complexity of MSK management and the variable outcomes. The progression of MSK in advanced stages appears to be influenced by a combination of pathogen-related factors, such as high microsporidial load with deep stromal penetration, and host-related factors, including a pronounced inflammatory response. Additionally, the limited effectiveness of topical PHMB may contribute to disease progression.