Causal mechanistic reasoning is a thinking strategy that can help students explain complex phenomena using core ideas commonly emphasized in separate undergraduate courses, as it requires students to identify underlying entities, unpack their relevant properties and interactions, and link them to construct mechanistic explanations. As a cross-disciplinary group of biologists, chemists, and teacher educators, we designed a scaffolded set of tasks that require content knowledge from biology and chemistry to construct nested hierarchical mechanistic explanations that span three scales (molecular, macromolecular, and cellular). We examined student explanations across seven introductory and upper-level biology and chemistry courses to determine how the construction of mechanistic explanations varied across courses and the relationship between the construction of mechanistic explanations at different scales. We found non-, partial, and complete mechanistic explanations in all courses and at each scale. Complete mechanistic explanation construction was lowest in introductory chemistry, about the same across biology and organic chemistry, and highest in biochemistry. Across tasks, the construction of a mechanistic explanation at a smaller scale was associated with constructing a mechanistic explanation for larger scales; however, the use of molecular scale disciplinary resources was only associated with complete mechanistic explanations at the macromolecular, not cellular scale.