Emotional well-being, social inclusion, and academic self-concept are crucial for students’ academic and socio-emotional development, and are seen as key factors for successful inclusion. Considering this relevance, the Perception of Inclusion Questionnaire (PIQ) has been developed as a short screening instrument to assess these three aspects—not only for research, but also for teachers to enhance students’ well-being in school and the selection of intervention goals. The present study aimed to evaluate the psychometric properties of the Spanish PIQ student version. Participants were 673 Mexican lower secondary school students (52% female, M_age = 13.25 years) who either attended inclusive classes (33%) or special schools (67%). 15% have been diagnosed as having special educational needs (SEN). Factorial and convergent validity and measurement invariance as well as mean differences based on students’ gender, diagnosis of SEN, and classroom setting were analyzed. The three-factor structure of the PIQ was confirmed, and the three scales (emotional well-being, social inclusion, academic self-concept) showed adequate internal consistency. Further, some evidence for convergent validity was shown. Strong measurement invariance was established, allowing for comparison across gender, SEN status, and classroom setting. Regarding gender, boys indicated higher levels of social inclusion and academic self-concept than girls. Students with SEN scored lower on all three subscales compared to students without SEN. Further, students with SEN in inclusive classrooms showed lower academic self-concepts compared to those attending special schools. Although more research is needed, the psychometric properties of the Spanish PIQ student version are encouraging for its potential for use in research and practice.