Students with autism spectrum disorder (ASD) experience various functioning and participation problems in higher education, which may cause difficulties such as drop out or low grade point averages. However, it remains unclear how often and during which teaching and evaluation methods the functioning and participation problems occur and which reasonable accommodations are effective in dealing with them. These gaps in the literature are addressed in this survey-based study. In total, 43 students with ASD, 30 student counsellors and 43 students without a disability of institutions of higher education in Flanders (Belgium) participated in the study. The results show that students with ASD most frequently experience problems with verbal and non-verbal communication, are oversensitive to change and have difficulty distinguishing the gist of the syllabus from the details. Furthermore, it is shown that, on average, these problems arise mostly during classical teaching and evaluation methods. Finally, the perceived effectiveness of reasonable accommodations is dependent on the functioning and participation problem experienced by the student with ASD in higher education. In conclusion, both personal and environmental characteristics should be taken into account when selecting and implementing reasonable accommodations for these students.