This paper examines the implementation of a student-teacher scientist partnership (STSP), focusing on the opportunities given to the students in the classrooms. The project in the study, the medicine hunt, aims to increase secondary-school students’ interest in science and understanding of research through authentic science problems, methods, and collaboration with researchers. The medicine hunt engaged 388 students in 18 school classes across Sweden. Video- and audio-recordings from one lesson in three different classrooms were analysed for i) how materials, class size and use of lesson time differ between the classrooms ii) what opportunities (i.e. learn scientific ways of working, inquiry, theoretical discussion and collaboration with researchers) are given to students in the different classrooms iii) differences in students’ attention and participation during the lesson. The variation in lesson time and number of students gave each teacher different possibilities to implement the STSP and variation in how the STSP was implemented was found. This is especially evident in the teachers’ foci in their introductions, and in the opportunities to engage in theoretical discussions. Despite differences, student engagement in terms of attention and participation was high in all classrooms throughout the lesson. Students in all classrooms practiced scientific ways of working (e.g. to select, describe and compare bacterial colonies, and to report findings) and took advantage of the collaboration with the researcher. Yet, opportunities for inquiry and theoretical discussion were low. The results suggest that it is important that teachers have sufficient content knowledge and enough time to engage in discussions with students to a deeper level than answering practical questions. How this links with the STSP implementation variation, engagement and participation will be considered.