Master of Science (M.S.) programs, including geography through geographic information science and technology (M.S. GIST), play a key part in training the science, technology, engineering, and math (STEM) workforce. A master's thesis has been a traditional part of geography programs, and across all kinds of disciplines the value of a thesis is well-recognized. However, delivering master's thesis supervision for large cohorts may result in lengthy completion times and poor completion rates. A growing literature focuses on master's thesis supervision across a wide array of disciplines, but no study focuses on the master's thesis for M.S. GIST programs. We offer a mixed-methods case study of a large, online M.S. GIST program showing how problems developed and were resolved over a 13-year period with program-wide structural reforms. Reform elements included increased attention to writing skills in admissions review, addition of writing instruction, earlier student engagement, staff engagement, faculty engagement, and development of thesis courses. Reforms shortened completion times and increased thesis completion rates while sustaining diversity and quality of thesis projects. Although this case study echoes many strategies found in the literature, it emphasizes that replication likely requires linking solutions together through structural reforms across a master's degree program.