Background: Self-reflection and e-learning represent two recent shifts in medical education, offering benefits for teaching clinical communication, a core component of medical training. Integrating reflection exercises into e-learning environments can encourage students to engage deeply with course content and their own experiences, fostering self-awareness, novel insights, and professional growth. However, few studies have explored how online learning environments might support students in reflecting on their learning experiences. In particular, research is lacking on how medical students perceive their learning experiences in online environments, including reflection, especially in the context of clinical communication training. This study examines how students approached structured reflective writing within an e-learning course on physician-patient communication to explore (I) the learning content addressed in students’ reflections and (II) the insights students gained through the course. Methods: First-year clinical medical students (n = 55) participated in an e-learning course, which consisted of three modules: communication basics, consultation structuring, and empathy and emotions. Each module included three guided prompts to encourage reflection. All participants composed nine written reflections. Qualitative thematic analysis of all 495 reflective texts was conducted to identify themes and insights. Results: The students engaged with core communication topics and developed greater self-awareness regarding their communicative practice. The reflections revealed challenges, perceived skill gaps, and new understanding. Five core themes were identified: 1. patient-centred communication, 2. conversation structure, 3. emotions, 4. learning experiences, and 5. attitudes. Themes 1–3 primarily described specific learning content and were closely related to the first research question, while themes 4 and 5 encompassed broader reflections on personal and professional development as well as intentions to apply lessons learnt in future practice, predominantly addressing the second research question. Conclusions: Our findings demonstrate that reflective writing within our e-learning fostered students’ metacognitive engagement, enhanced their awareness of communication nuances, and supported transformative learning processes. Students not only recalled central course content but additionally explored topics such as dealing with their own uncertainty by examining their beliefs, attitudes, and challenges, recognising the role of communication in professional development. These findings align with previous research and highlight the potential of reflective writing to bridge theory and practice, contributing to students’ growth as empathetic and resilient healthcare professionals.