Students' learning environments often change during school career, due to school transitions and the introduction of educational innovations, causing discontinuity in teaching and learning. Success of students entering a new learning environment depends in part on their prior expectations of education, as these influence later perceptions. Heterogeneity between students, however, needs to be acknowledged. In seeking to determine expectation profiles and their potential linkage to divergent perceptions of education, we longitudinally surveyed secondary school students regarding their expectations before, and their perceptions one and two years after entering an innovative learning environment. We identified three expectation profiles that differed in terms of students' motivation, learning conceptions, and affective strategies: optimistic, moderately optimistic, and pessimistic. For each profile, perceptions developed differently over time, with the moderately optimistic and pessimistic students being at risk in different ways. Results imply that expectations deserve a more prominent place when designing innovative learning environments.