To study the role of multilayer amniotic membrane transplantation (AMT) in the treatment of non-healing corneal ulcers. This study included 28 patients with non-healing bacterial corneal ulcers. AMT was performed using the 'overlay on-inlay' technique'. The outcome was assessed in terms of best corrected visual acuity (BCVA), corneal re-epithelization, graft/tissue edema and vascularity, graft melting, graft retraction, infection of graft and surface necrosis. The success rate of ulcer healing was 82.1 % (23 patients) 1 month after surgery, 78.5 % (22 patients) after 3 months and 75 % (21 patients) after 6 months. In the early post-operative period, BCVA deteriorated in all patients (perception of light to hand movement) but improved later. In 26 of the 28 patients (92.8 %) graft retraction occurred after 1 month and neovascularization was seen in 17 of the 28 patients (60.7 %). Multilayer AMT using an overlay on-inlay graft in non-healing bacterial corneal ulcers is a good option in terms of ulcer healing and symptomatic improvement.