This study presents an inquiry-based teaching approach using a rich methodology involving STEM (science-technology-engineering and mathematics) projects, developed using a cooperative way to work between schools and research centres. We describe the teaching pattern scenario with students, teachers, and scientists. We also illustrate the learning process, conducted through two inquiry-based problems in Biochemistry, the mutagenesis process and the transgenesis effects caused by inoculation of bacteria. The teaching sequence, as well as the scientific knowledge and students' competencies involved, are shown. We then analyse the students' and teachers' perceptions in this scenario regarding the development of students' STEM learning through their inquiry skills promoted and concerning predictors to vocational careers involved (students' identities as potential scientists, scientific attitudes, social implications towards science or students' agency). Finally, we add some conclusions and contributions to teaching STEM education, related to factors of the design teaching scenario that bring connections with the interests and motivations of students, such as the relevance of the projects to evoke understanding of processes or causal relationships of content or the teacher's professionalisation supported by a proper allocation between scientists and teachers.