BackgroundSome students are more motivated that others in one or multiple academic domains, and more motivated in one domain than another. These inner hierarchies of motivational beliefs are important because they can influence students’ achievement and study or career choices. However, little is known about the heterogeneity in inner hierarchies of motivational beliefs during early secondary school, when motivation typically declines. AimsThe aims of this study were to (1) identify profiles of self-concept and intrinsic value in mathematics and German during the first two years of secondary school, (2) explore stability and change in these profiles, and (3) explore how profile membership relates to student competence and gender, and perceived teacher behaviour. SampleParticipants were 721 secondary school students from Germany. MethodsStudents completed measures of self-concept, intrinsic value, and competence in grades 5 and 6, and measures of perceived teacher behaviour in grade 5. Data were analysed using latent transition analysis. ResultsFive profiles characterised by inter- and intraindividual differences in self-concept and intrinsic value were identified. Membership in these profiles was relatively stable. Inner hierarchies of self-concept and value were related to competence, with students demonstrating higher competence in domains they were more motivated in. Gender and perceived teacher behaviour were related to profile membership, but not profile transitions. ConclusionsWhen supporting the motivational development of students during the first two years of secondary school, teachers may need to adopt a holistic approach that recognises the heterogeneity in students’ inner hierarchies of motivational beliefs.