This paper presents a case study of the experiences under the Indonesian Mathematics and Science Teacher Education Project (IMSTEP) concerning in-service teacher training through the practice of lesson study collaboratively conducted by schools and universities. The purpose of the case study is two-fold: first, to examine the changes in teaching practices through the introduction of lesson study under IMSTEP; and, second, to uncover the challenges faced in implementing lesson study under IMSTEP. The results of the analysis revealed that the lessons underwent three changes: (1) a change in the academic base of the lessons, brought about by close liaison between university faculty members; (2) a change in the structure of the lesson by the introduction of experiments or manual activities and discussions; and (3) a change in the reactions of students during the lesson. However, two insights emerged during the IMSTEP case study as tasks to be addressed in order to further develop the practice of lesson study. First, the participants of the collaborative lesson study were likely to have a narrowed interest in probing the learning processes of the students, in comparison with focusing on teaching methodologies more generally. The limited interests of both the university faculty members and the targeted teachers in the learning processes of students can be shown in the following three ways: the dominance of interests in teaching models, the lack of attention to detail in the learning processes of students and the lack of questioning the reasons for the mistakes and misconceptions of students. The second insight was the necessity to involve the entire school in lesson study.