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To assess the pattern of microbial keratitis after accelerated corneal collagen cross-linkage (aCXL) in patients with keratoconus.The medical records of cases of keratoconus that underwent aCXL from June 2014 to May 2017 were reviewed. Cases that developed microbial keratitis after aCXL were included in the study. The clinical, microbiological profile and the treatment outcomes were evaluated.Of 532 eyes that underwent aCXL, 7 cases developed microbial keratitis during the study period. Median age at presentation was 11 years (range 8–17). Association with vernal keratoconjunctivitis was noted in 57.1% of cases (n = 4/7). The median time at the onset of infection was 3 days after aCXL (range 1–4). Microbiological reports revealed mixed infection in 3 cases [coagulase-negative Staphylococcus (CoNS) + Aspergillus fumigatus, Staphylococcus aureus and Mucor spp., Staph. aureus and Acanthamoeba], Staph. aureus in 2 cases, and CoNS and Alternaria spp. in 1 case each. Resistance to fourth-generation fluoroquinolones was noted in 83.3% of cases of bacterial keratitis (n = 5/6). All cases were initially managed with empirical antibiotic treatment that was later tailored based on microbiological reports. One case eventually required therapeutic penetrating keratoplasty for corneal perforation. At 6 months, the corrected distance visual acuity was >6/60 in 3 cases while 4 cases had corrected distance visual acuity <6/60.Microbial keratitis after aCXL is rare; however, the infection tends to be severe with high preponderance of mixed infection and resistance to fourth-generation fluoroquinolones.