Many science curricula and standards emphasise that students should learn both scientific knowledge and the skills associated with the construction of this knowledge. One way to achieve this goal is to use inquiry-learning activities that embed the use of science process skills. We investigated the influence of scientific reasoning skills (i.e. conceptual and procedural knowledge of the control-of-variables strategy) on students' conceptual learning gains in physics during an inquiry-learning activity. Eighth graders (n = 189) answered research questions about variables that influence the force of electromagnets and the brightness of light bulbs by designing, running, and interpreting experiments. We measured knowledge of electricity and electromagnets, scientific reasoning skills, and cognitive skills (analogical reasoning and reading ability). Using structural equation modelling we found no direct effects of cognitive skills on students' content knowledge learning gains; however, there were direct effects of scientific reasoning skills on content knowledge learning gains. Our results show that cognitive skills are not sufficient; students require specific scientific reasoning skills to learn science content from inquiry activities. Furthermore, our findings illustrate that what students learn during guided inquiry activities becomes visible when we examine both the skills used during inquiry learning and the process of knowledge construction. The implications of these findings for science teaching and research are discussed.