The present report describes a case of semi-autologous corneal transplantation with bilateral surgery using two operating microscopes simultaneously. An 86-year-old man with history of six prior failed penetrating keratoplasties in his right eye presented with decreased vision. His other eye was deeply amblyopic but had a clear 30-year-old Castroviejo-square graft with an endothelial cell count of 803 cells/mm2. A semi-autologous graft was performed from the left eye to the right. Surgery was performed simultaneously on both eyes by two different surgeons using a standard ophthalmic operating microscope as well as a second ENT microscope. Upon trephination of the right failed corneal graft, vitreous opacities were noted and sent for culture. The semi-autologous tissue was directly transferred from the left eye to the right without any storage in preservation media to avoid endothelial cell loss. The semi-autologous graft remained clear in the immediate postoperative period. However, the vitreous cultures grew coagulase-negative Staphylococcus. Despite all efforts, the patient eventually developed a retinal detachment and vision in the right eye decreased to light perception. Autologous penetrating keratoplasty is an option for patients with loss of corneal function in a potentially seeing eye and a clear cornea in a contralateral eye with poor visual potential due to non-corneal disease. This case is unique in that part of the autologous penetrating keratoplasty had an old square graft in the center and corneal transplant surgery was done simultaneously in both eyes. It also highlights chronic indolent endophthalmitis as a potential cause of multiple graft failures.