The experiences of marginalized students in higher education are often examined through a single-identity lens, overlooking how other identities can jointly shape their college experiences. In particular, little is known about how holding an additional marginalized identity affects the experiences of students with disabilities in STEM. We surveyed 947 undergraduates (379 with disabilities) at 85 institutions across the United States to (i) identify marginalized identities that are highly represented among students with disabilities and (ii) examine whether holding an additional marginalized identity corresponds to distinct experiences among students with disabilities. We found that LGBTQ+, nonbinary, and white students were overrepresented among students with disabilities relative to students without disabilities, with 50% of students with disabilities identifying as LGBTQ+. LGBTQ+ students with disabilities reported significantly more negative academic and social experiences than non-LGBTQ+ students with disabilities. These findings highlight some of the heterogeneity that exists in the experiences of students with disabilities, underscore the need to address the challenges faced by LGBTQ+ students with disabilities, and suggest that some patterns previously attributed to disability alone could be partly explained by the experiences of LGBTQ+ students.