Anxiety, depression, and suicidality are major concerns among college students, though less is known about these constructs in autistic college students. Given the rising number of autistic individuals entering post-secondary education, adequate measurement and diagnosis of anxiety, depression, and suicidality is necessary to provide clinical care to this population. While the Generalized Anxiety Disorder--7 (GAD-7) and Patient Health Questionnaire--9 (PHQ-9) are commonly used in university settings, these instruments have not been psychometrically evaluated in autistic college students. The current study examines the differential psychometric properties of the GAD-7 and PHQ-9 utilizing invariance testing via structural equation modeling in a sample of self-identified autistic (n = 477) and non-autistic (n = 429) university students. Results showed that although the GAD-7 is invariant, the PHQ-9 was mostly invariant, with one item displaying non-invariance. Specifically, the PHQ-9 item assessing suicidality was found to be non-invariant at the metric level, indicating that autistic and non-autistic college students interpret this question differently. Future investigators should continue to assess the appropriateness of using common screening measures, originally created for non-autistic people, in autistic populations.