Glaucoma and cataract are the leading causes of blindness worldwide. The incidence of both diseases is increasing with aging population. This prospective interventional study to investigate and compare the early effect of phacoemulsification, subscleral trabeculectomy, and combined phaco-trabeculectomy on the corneal endothelium in glaucomatous patients. Our study was conducted on 30 eyes of glaucoma patients, 10 eyes on whom combined phacotrabeculectomy was performed (Group I), 10 eyes on whom trabeculectomy was performed (Group II), and 10 eyes on whom phacoemulsification was performed (Group III). In preoperative and post-operative visits, each patient had specular biomicroscopic examination measuring corneal endothelial cell density (CECD), coefficient of variation (CV) and hexagonality (HEX) by the use of non-contact specular microscope (Nidek CEM-530, NIDEK Co., Ltd. Japan). CECD was postoperatively significantly reduced in all groups when compared to preoperative values, however, there was an insignificant difference in-between groups. Postoperatively HEX and CV showed insignificant difference when compared to preoperative data. In conclusion, phacotrabeculectomy is a safe and effective procedure causing no additional risk for corneal decompensation compared to phacoemulsification or trabeculectomy alone.