This study focuses on the psychometric properties of Young Schema Questionnaire-Long Form (YSQL2, Young in Cognitive therapy for personality disorders: a schema-focused approach. Professional Resource Exchange, Sarasota, 1990) in a large Flemish sample of inpatients with an eating or substance use disorder. Eating disorders (ED) and alcohol/substance use disorders commonly co-occur and have been linked by several theoretical models, making it important to study the psychometric properties of the YSQL2 in these populations. In the present study, a confirmatory factor analysis was used to investigate the latent structure of the YSQL2 in a sample of ED patients (n = 218) and alcohol and substance use disorder (AD) patients (n = 351). Internal consistency, divergent, and convergent validity between early maladaptive schemas (EMS) and personality disorder symptoms were investigated. Results confirm the 16 factor structure of the YSQL2 as well as good internal consistency for all scales. Significant gender differences were observed for some scales within the AD sample, along with different patterns of correlations between age and select scales within the ED and AD groups. Convergent validity was supported by similar elevations on the schema scales and personality disorder symptoms in both subgroups separately. The YSQL2 appears to be a valid instrument to assess EMS among Flemish inpatients with an ED or an alcohol disorder.