Students' well-being has become an important part of education policy in many countries. Research shows that well-being contributes to students' engagement in school, thereby supporting academic achievement. However, prior research has often neglected the interplay and multidimensionality of the constructs. The present study applied a six-dimensional student well-being model and a three-component school engagement model to untangle the differential associations of positive and negative well-being dimensions with the components of school engagement and academic achievement. Longitudinal mediation analyses using a sample of N = 754 Swiss secondary school students and two measurement points (Grade 7 and Grade 8) revealed differential associations of well-being dimensions with engagement components, but no direct effects on academic achievement. Enjoyment in school, as a dimension of student well-being, had an indirect effect on academic achievement, mediated through behavioral engagement. The results imply that fostering students' enjoyment in school may be a promising strategy to enhance their behavioral engagement and, in turn, promote their academic achievement.