Understanding students' capacity to direct their learning in school and beyond has been a sustained area of interest for practising science teachers, policy-makers, and educational researchers. This paper presents results from a longitudinal quasi-experimental study carried out to examine changes in students' self-reported levels of self-regulatory processes and related motivations in science through taking part in an inquiry-based learning programme, the CREST programme. The study included a total of 178 students (aged 12-13) and was conducted in an individual school in Scotland. Previously published and validated measures of self-regulatory processes and related motivations were included as dependent variables and student classroom allocation was used as the independent variable in order to investigate the presence of any differences between the nine CREST classes in terms of changes on the measured variables. Results showed that overall, students experienced significant increases in levels of self-regulated learning, self-determination, self-efficacy, intrinsic motivation, and overall science motivation through participation in CREST. By contrast, a reference control class of students not taking part in the programme showed no significant changes on any measured outcomes. The findings also revealed no significant differences among the nine classes that participated in CREST in terms of changes on the outcome variables.