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Research skills and research self-efficacy are important outcomes that should change through doctoral training yet are often conflated with one another. Guided by social cognitive theory, we examined how self-efficacy and performance-based assessment of research skills aligned with one another, and the extent to which self-efficacy assessments deviated from performance-based assessments over time. Over time, students often overestimated their growth on research skills relevant for developing research paper introductions yet underestimated their growth on research skills relevant for research paper analyses and conclusions. Faculty interaction quality and peer interactions reduced both overestimation and underestimation of growth, implying that building peer relationships and having quality faculty interactions are important for more accurate self-assessment of research skills as they develop over time.