Students with disabilities (SWDs) educated in traditional public schools alongside general education students (GENs) typically move to middle school in sixth grade, rather than continuing in a K-8/12. The documented negative effects of this move on GEN academic outcomes suggests similar negative—and perhaps larger—effects on SWDs. Using an instrumental variables strategy and NYC data on nine cohorts of students, we find the middle school transition causes a 0.30 (0.16) standard deviation decline in SWD math (ELA) performance and increases grade retention. Low-income SWDs and SWDs with a specific learning disability or emotional disturbance fare worse. However, the move does not widen the SWD-GEN gap, suggesting the need to ease the middle school transition for all students.