The “instituto-escuela” model (a single-structure public educational model, comprising ISCED 0-2) has been expanding in Catalonia since 2010 in its attempt to cope with school failure and dropout and facilitate educational continuity in different educational settings. By using the external large-scale assessments of the end-of-stage system (6th grade of Primary Education and 4th year of Lower Secondary Education), developed by the Higher Council for the Evaluation of the Educational System of Catalonia, a comparative research is designed which combines cross-sectional and longitudinal analysis of the results with the aim of analyzing the capacity of “institutos-escuela” in complex settings to improve academic results compared to those students attending multiple public schools (students transiting from primary public schools to public lower secondary schools). Although students from “institutos-escuela” obtain lower scores than those attending multiple public schools, longitudinally, students from “institutosescuela” significantly improve their results in Spanish language and scientific-technological competence at the end of Lower Secondary Education in relation to Primary Education. A positive effect is shown in reducing the percentage of students who do not acquire basic skills at the end of Compulsory Secondary Education.