Inquiry learning relies on students’ engagement, which is driven by their cognitive and motivational characteristics. The role of student characteristics for inquiry learning has been sparingly investigated and only from a variable-oriented perspective. In contrast, this study employed a person-centered approach to investigate the combined influence of students’ cognitive and motivational characteristics in relation to experimentation skills and conceptual understanding during guided inquiry learning. All students (N = 110, Mage = 12.07) attended a lesson about photosynthesis and worked on a structured inquiry task individually. Experimentation skills were measured by the proportion of controlled experiments that students conducted. Conceptual understanding comprised students’ written argumentation and conceptual knowledge posttest scores. We identified three distinct clusters, based on students’ prior knowledge, self-concept, and interest – Underestimating, Struggling, and Strong. Although Struggling students conducted a significantly higher proportion of controlled experiments than Strong students, Underestimating and Strong students outperformed them in the conceptual knowledge posttest. We found no differences in argumentation quality. These findings suggest that highly guided tasks might not be equally suitable for students with different levels of interest, prior knowledge, and self-concept and attest to the benefits of using person-oriented methods. Therefore, students’ motivation needs to be considered in addition to their prior knowledge when designing guidance for inquiry learning.