In the present study teacher students' contextual learning experiences were examined longitudinally in authentic study environments using the contextual activity sampling system, a means of mobile-supported experience sampling. The students' (n = 9) experiences were first recorded during a 2 week period in their first year of study. The same measurements were repeated again for a 2 week follow-up in the second year, accompanied by interviews before and after the follow-up. The first year of study consisted mostly of lectures and ordinary small-group work, whereas the second measurement period ran parallel to the completion of an intensive inquiry-based project, which was the focus of the present study. A multivariate analysis of variance revealed that studying during the inquiry-based period produced stronger experiences of being challenged as well as negative affects than the teacher-centered period. The participants' experiences of competence, commitment and positive affects did not differ during the two periods. However, interview data indicated that the participants enjoyed the inquiry-based period and that the work was intensive. Contextual data and interviews were also used to describe students' experiences during one particular study session during the inquiry-based project. The results suggest that negative affects may be an essential part of the process of gradually learning to take responsibility for both individual and collaborative learning processes. Possibilities for using experience-sampling methods to analyze collaborative learning are also discussed.