Middle school transitions are increasingly required, despite documented negative effects on general education students (GENs). We explore if and how the move to middle school differentially affects students with disabilities (SWDs), a large and low-performing group of students. Using an instrumental variables strategy and NYC data on nine cohorts of students, we find the middle school transition causes a 0.29 standard deviation decline in SWD math performance, a 0.16 standard deviation decline in ELA performance, and a one percentage point increase in grade retention. However, after accounting for potential mediators (e.g. peer cohort stability) effects are similar for SWDs and GENs, suggesting the need to ease the middle school transition for all students.