Aims: To investigate the histopathology of the fibrous capsule around Ahmed glaucoma valves (AGVs) implanted with adjunctive amniotic membranes in rabbits. Methods: AGV implantation with or without adjunctive amniotic membrane was performed in a single eye of 20 albino rabbits. The upper surface of the AGV body was covered with amniotic membrane in the study group. After 2 months, histology was used to compare the thickness and characteristics of the fibrous capsule, transdifferentiation of myofibroblasts, and density of blood vessels and leukocytes between the study and control groups. Results: The fibrous capsule along the roof of the bleb was composed of compact collagen fibers with minimal vascularization in the control group. In contrast, in the study group, the fibrous capsule was looser and had a more disorganized collagen architecture. The thickness of the fibrous capsule and the myofibroblast layer was significantly thinner in the study group than in the control group (p < 0.001). The number of CD31-positive blood vessels did not differ between the two groups (p = 0.235). CD45-positive inflammatory cells were more frequently observed in the study group than the control group (p = 0.001). The groups did not differ in the thickness of the fibrous capsule or myofibroblast layer, or the density of blood vessels and leukocytes along the floor of the bleb. Conclusions: Adjunctive amniotic membranes could reduce the risk of encapsulation and aqueous outflow resistance by altering the tissue response to implanted AGVs and subsequent formation of a loose thin capsule.