Over the last decades, a global trend towards inclusive education is to be noted. In Flanders, the Dutch-speaking part of Belgium, 15.17% of all the students with special educational needs (SEN) are fully included in mainstream settings. Based on former studies we know that especially students with ASD experience social difficulties at the start of mainstream secondary school, e.g., students with ASD have significantly less reciprocal friends than their typically developing classmates. However, less is known about the quality of their friendships during this time. This study focuses on the quality of all reciprocated friendships of students with autism (ASD), students with motor and/or sensory disabilities and typically developing students at the start of mainstream secondary school. The study included 1379 typically developing students, 65 students with ASD and 50 students with motor and/or sensory disabilities of 100 different classes and 56 schools. In general, the three groups did not differ in friendship quality. The number of friends did not affect friendship quality and in general, students with SEN and their friends shared the same opinion on the quality of their friendships. Only students with ASD reported lower levels in intimacy than typically developing students and their typically developing friends.