This paper describes how a school-industry partnership can define and frame problem-based science teaching developed for lower secondary school. Among the identified positive outcomes was that students engaged in working with the authentic problems. Further, the student’s possibilities for building relations with the employees during the course was of central importance e.g. when they received feedback. Challenges reflected that the teachers and students were uncomfortable with the innovative problem-based teaching method and had a curricular-dominated view on science education. This was expressed in their concerns about what they see as indistinct connections between work phases and a lack of scientific content. It is proposed to use pedagogical link-making as a tool to create spatiotemporal coherence for the students and make connection between scientific concepts based on examples from the study. Link-making may be particularly relevant when the complexity of teaching increases as in school-industry partnerships.