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. Using an instrumental variables strategy and New York City (NYC) data on nine student cohorts, we find the middle school transition causes a 0.29 SD decline in SWD math performance, a 0.16 SD decline in English language-arts (ELA) performance, and a one percentage point increase in grade retention. Accounting for potential mediators (e.g., peer cohort stability) does not substantially explain estimated effects on SWD performance. However, the middle school transition has similarly large negative effects on GENs, suggesting the need to ease this transition for all students.