A 26-year-old farmer underwent deep anterior lamellar keratoplasty (DALK) for keratoconus. After 3 months, he presented with interface keratitis. Medical treatment failed and he underwent a repeat DALK. Microbiological scrapings from the interface revealed an infection caused by non-tuberculous mycobacteria. Despite the use of intensive antibiotic therapy and a repeat lamellar keratoplasty, the infiltrates recurred. The patient underwent therapeutic penetrating keratoplasty. Microbiology of the corneal tissue revealed growth of Mycobacterium chelonae, and on histopathology, the acid-fast bacilli were noted to be located deep at the pre-Descemet level. There was complete resolution of the infection with no episodes of recurrence and final best-corrected visual acuity was 20/40 at 1 year of follow-up. Medical therapy is unlikely to succeed in post-DALK interface keratitis and penetrating rather than lamellar keratoplasty may be considered the surgery of choice.