The general academic disadvantage faced by children of immigrants is already a well-documented regularity in Spain. However, there is no reliable knowledge on how academic achievement is ethnically stratified and more research is needed to understand the determinants behind these achievement gaps. This study aims to further knowledge of both issues by using the Spanish General Educational Diagnostic Assessment data (n = 22,267). Students originating from non-European developing countries and two European groups with a lower socioeconomic profile (Romanian and Portuguese) have the largest gap compared to native students, while Western Europeans equal the achievement of natives. Results from multilevel analyses show that social origin and the language spoken at home have a significant impact on the gaps, while the school factors have a limited impact.