The purpose of this study is to compare the effects of inquiry-based learning and the regular science curriculum on students' learner autonomy and conceptions of learning. The students in the experimental group engaged in inquiry beginning with structured, continuing with guided and ending with open, while the students in the comparison group followed the materials used in the regular science curriculum. All students individually participated in three times 40-minute weekly sessions during a 14-week period. Data were gathered through individual interviews which were conducted with six students in total (three from the experimental group and three from the control group). Results showed that the inquiry-based learning caused students to move from participatory roles towards constructive ones, whereas the regular science curriculum did not alter participatory roles. Inquiry-based learning also enabled students' reproductive conceptions to change towards constructive conceptions. Students in the control group did not change their reproductive conceptions.