Purpose: To report the management of a case of Baerveldt tube (BVT) implantation in an eye with Mooren's ulcer. Methods: A 31-year-old male with advanced glaucoma and uncontrolled pressures required BVT implantation despite maximal medical therapy. A concurrent diagnosis of Mooren's ulcer affecting 270 degrees of cornea required significant adaptations to surgery due to a limited area of healthy conjunctiva and limited view of anterior segment. Results: Detailed preoperative counselling was essential, including education about the increased risk of scleral perforation. BVT was implanted successfully; however, due to inflammation, we encountered increased bleeding and fragile tissue. Adaptations to surgery were made that affected peritomy location and size, conjunctival handling and position of intraluminal stent suture underneath conjunctiva. Ocular surface protection was maintained throughout. High-dose oral steroids and mycophenolate mofetil were required postoperatively, and the patient achieved good IOP control off all drops. Conclusion: We demonstrate the challenges faced when performing glaucoma surgery on patients with coexisting ocular surface inflammatory pathologies.