Purpose The purpose of this study was to use Triton® SweptSource OCT to evaluate the morphology of blebs formed when eyes are treated with XEN® implants and to compare these with the blebs in successfully functioning eyes after trabeculectomy (TB) and with eyes of healthy controls. Methods A cross-sectional, observational study. We analyzed 25 eyes, 15 after TB and 10 with XEN® implants, comparing them with 23 healthy eyes (controls). We evaluated the conjunctival morphology of the eyes using AS-OCT.The main parameters evaluated were bleb height, sub-epithelial fibrosis, epithelial thickness, and changes in intraocular pressure (IOP). Results We found that the filtering blebs formed in eyes in which a XEN® stent was implanted were significantly flatter (bleb height 417 ± 183 μm) than the blebs formed in TB eyes (bleb height 618 ± 256 μm, p < 0.05). Moreover, sub-epithelial fibrosis did not develop in any of the blebs produced by the XEN stent, whereas some fibrosis was evident in 40% of the blebs that formed after TB (p < 0.05). The epithelium was thicker when the XEN implant was used (65 ± 18.5 μm) than when eyes underwent TB (60 ± 17.7 μm), and it was thicker than in control eyes (51 ± 9.7 μm, p < 0.05). Moreover, the decrease in the IOP induced by the XEN® stent (− 8.5 ± 5.3 mmHg) was similar to that produced by TB (− 8.8 ± 5.2 mmHg, p > 0.05). Conclusions Filtering blebs obtained after the introduction of a XEN® stent were morphologically distinct to those produced by TB, and they are more similar to the healthy conjunctiva.