Purpose: The purpose of this paper is to assess and compare school well-being (SW) and emotional well-being (EW) among Romanian, Moroccan and Spanish youth, to determine the degree of relation between EW and scholar well-being. Design/methodology/approach: The paper employed cross-sectional research with cluster sampling in two primary schools and seven secondary schools. The questionnaire Kidscreen-27 was distributed to a sample of 1,840 Romanian, Moroccan and Spanish students aged between 10 and 19 years old. Data analysis was conducted with the software package SPSS, version 21. Findings: EW shows significant gender (gender gap) and origin inequalities (lower performance for the Moroccan community). However, well-being in school shows positive results for the Moroccan students and women. Moreover, EW and well-being at school are presented as related and co-linear variables with a predictive power over one another. Research limitations/implications: Understanding cultural expressions in heterogeneous cultures is a very complex task. Despite the cultural adaptation and validation of instruments, the applied surveys could not consider cultural differences. Practical implications: The paper underlines that gender and origin remain decisive and determinant for adolescent health. However, the school can have positive effects on the well-being of immigrants. The reasons for well-being need to be explored, and it would be useful to develop educative strategies to implement transcultural EW and SW. Originality/value: It is the first study about SW and EW of immigrants in Spain that explains a better SW in immigrants groups. It is also relevant for applied school intervention to predict the relationship between EW and SW.