In this study, we explore how two different prompt types within an online computer‐based inquiry learning environment enhance 392 7th grade students’ explanations of evolution with three teachers. In the elaborating prompt condition, students are prompted to write explanations that support the accepted theory of evolution. In the competing prompt condition, students are prompted to write explanations that differentiate two views of evolution associated with Darwin and Lamarck. Data sources included a pretest and posttest, an embedded item, observations, logged teacher guidance, and teacher interviews. Findings show similar pretest to posttest gains in students’ understanding of evolution for both conditions, but this pattern was not uniform across all three teachers. For one teacher, students who received competing theory prompts produced significantly higher gains than those who received elaborating theory prompts. A closer look at embedded student work reveals a higher degree of teacher participation (i.e., grading and guidance) than for the other teachers. Our findings illustrate how helping students distinguish between competing scientific claims can support learning in an inquiry unit, but may require a higher degree of teacher participation and reinforcement. We discuss the implications of these findings for enhancing students’ scientific explanations. © 2016 Wiley Periodicals, Inc. J Res Sci Teach 53: 1341–1363, 2016