OBJECTIVE To examine hypotony-associated foveal lesions (FovLs) using optical coherence tomography, and to assess the risk factors of visual deterioration after glaucoma filtering surgery. METHODS Parameters that may be associated with postsurgical deterioration of visual acuity were retrospectively studied in 44 eyes of 44 patients who experienced postsurgical intraocular hypotension ≤6 mmHg between 2015 and 2019. RESULTS Six eyes (14%) had FovLs, such as detachment of photoreceptors (5 eyes, 11%) and acquired vitelliform lesions (1 eye, 2%) at 3 months after trabeculectomy. Logistic regression analysis revealed that hypotony maculopathy (P = 0.0141 at 3 months) and FovLs (P = 0.0486 and 0.0296 at 3 and 12 months, respectively) were significant risk factors for Visual acuity loss after trabeculectomy. The FovLs were located just behind the Müller cell cone. Visual acuity at 3 and 12 months after surgery in patients with FovLs was significantly lower than in those without FovLs (P = 0.0013 and P = 0.006, respectively). Epiretinal membrane was more common in eyes with FovLs (5 of 6 eyes, 83%) than in eyes without FovLs (7 of 38 eyes, 18%; P = 0.0037). CONCLUSIONS Müller cell cone-associated FovLs lead to long-lasting visual acuity loss after filtering surgery.