Purpose: To compare the postoperative complications and clinical outcomes of Descemet membrane endothelial keratoplasty (DMEK) and Descemet stripping automated endothelial keratoplasty (DSAEK) in eyes with previous glaucoma filtering surgery. Methods: In this retrospective comparative case series, we analysed postoperative visual acuity and intraocular pressure, graft survival, rate of graft detachment and/or dislocation, number of rebubbling and/or graft repositioning procedures, and graft rejection or failure (primary and secondary). Results: Sixteen eyes with DMEK and 80 eyes with DSAEK with previous glaucoma surgery were studied. The results were recorded at 3 and 12 months postoperatively. No statistically significant differences in postoperative visual acuity were found between the two groups at any stage of the follow-up. Intraocular pressure was lower in the DMEK group at the follow-up stage of 3 (p = 0.0022) and 12 months (p = 0.0480). Visually significant graft detachment was recorded in 31.3% and 22.5% of DMEK and DSAEK cases, respectively (p = 0.4541). All DMEK detachments (n = 5) were managed with slit-lamp rebubbling. Out of 18 graft detachments in the DSAEK group, 2 grafts were observed due to small graft detachment, 6 large graft detachments underwent rebubbling performed in the operating theatre, and 10 eyes needed primary graft repositioning for graft dislocation. Conclusions: DMEK is a feasible option to treat endothelial failure in complex eyes with previous glaucoma surgery. In the DMEK group, visual acuity outcomes and possibly postoperative intraocular pressure control were better compared with the DSAEK group.