Summary Guided by Self-Determination Theory, this study explored how different characteristics of student-centered learning environments relate to first-year students’ basic psychological needs satisfaction, motivation, and well-being across three Health Professions Bachelor’s programmes (A, B, and C). While all programmes used a problem-based learning approach, Programme C stood out by allowing students to select their own courses and conduct research on a topic of interest. Survey results (N=202) showed that Programme A students reported lower autonomy satisfaction compared to Programme C, and lower autonomous motivation compared to Programme B. Qualitative findings from focus groups supported the quantitative results, revealing that autonomy-supportive elements such as having choice, learning materials with relevance, and peer interaction fostered motivation, whereas lack of guidance and inappropriate assessments limited it. The study highlights the importance of offering meaningful choice, constructive support, and real-world relevance to promote autonomous motivation in health professions education. About the Dataset The dataset includes both quantitative and qualitative data. The quantitative survey dataset comprises responses from 202 first-year students across three Bachelor’s programmes, capturing measures of autonomy, competence, relatedness satisfaction, autonomous motivation, controlled motivation, and well-being. The first sheet “survey responses” in the excel dataset contains participants’ responses to the survey, and the second sheet “survey items” shows survey items and their corresponding questions and variables measured. The qualitative data comes from focus group discussions held in each programme (4, 4, and 3 participants respectively), which are transcribed texts including the initial codes from the authors.