Hypothesis-based reasoning with conditionals is a skill that is required for engaging in integral activities of modern elementary school science-curricula. The teaching of this skill at this early stage of education, however, is demanding, particularly in whole school classes in which it is difficult to adapt teaching to children's individual needs. We examine whether a scaffold that is static yet tailored to the context, in which the teacher explicitly models the reasoning process, manages to meet students' individual cognitive preconditions for learning this skill. Within an inquiry-based learning setting, N = 143 third-graders underwent either an experimental condition in which they received the explicit scaffold, or a control condition in which they did not receive this specific scaffold. Employing a latent transition analysis and a general additive model, it is examined how the additional scaffold interacted with students' prior knowledge, inhibition ability, and logical reasoning judged by their own teachers. It is found that the additional scaffolds managed to meet the needs of students with little prior knowledge; under the control condition, students with little prior knowledge showed decreased learning achievement, whereas under the experimental condition, students with differing prior knowledge learned to comparable extent and on a higher level. The scaffolds also almost fully diminished a disadvantage for students with lower teacher-judged logical reasoning, and supported students with high inhibition ability in mastering the most difficult aspect of reasoning based on irrelevant evidence. Implications for science education are discussed.