This study examines profiles of school motivation and emotional well-being and their links to academic skills (reading and math) among adolescents (N = 1629) at the end of comprehensive school (age 15–16). Using a person-centered approach (latent profile analysis), five distinct profile groups were identified. Three of the identified groups had a flat profile in motivation and well-being but at different levels. The first group manifested high motivation and well-being (n = 178, 11%); the second group was average in both (n = 1107, 68%); and the third had low motivation and well-being (n = 121, 7%). Two groups had mixed profiles; one group manifested only low motivation (n = 140, 9%) and the other only low well-being (n = 83, 5%). A comparison of the profile groups in terms of academic skills indicated that low school motivation was linked to poor math and reading performance, whereas low emotional well-being was linked to poor math and reading performance only when accompanied by low school motivation. The association between poor math skills and low motivation suggests that, when planning support for students, those with math problems or comorbid math and reading problems are especially at risk for low motivation and need support in both academic skills and motivation.