The Department of Chemistry at Duke University has endeavored to expand participation in undergraduate honors thesis research while maintaining the quality of the learning experience. Accomplishing this goal has been constrained by limited departmental resources (including faculty time) and increased diversity in students' preparation to engage in the research and writing processes. Here we assessed the relationship between iterative changes in pedagogical and mentoring support of honors research that efficiently employed departmental resources (including the chemistry thesis assessment protocol, ChemTAP) and students' scientific reasoning and writing skills reflected in their undergraduate theses. We found that, although we cannot disentangle some gradual changes over time from specific interventions, students exhibited the strongest performance when they participated in a course with structured scaffolding and used assessment tools explicitly designed to enhance the scientific reasoning in writing. Furthermore, less prepared students exhibited more positive changes.