Difficult clinical encounters pose emotional and behavioural challenges for medical students. Unless resolved, they threaten students' professional competence and well-being. Learning how to humanistically interact with patients perceived as "difficult" is an important component of the developmental process that underlies professional identity formation (PIF). This study used thematic analysis to examine reflective essay data from the same set of students (N = 69), first in their third year and then in their fourth year of training at a US public medical school. Analysis focused on how student perceptions of patients', preceptors', and their own behaviour, attitudes, and emotions in difficult patient care situations evolved over time, and how such evolution contributed to their professional growth. Students identified clinical predicaments influenced by their own emotions and behaviour, as well as those of patients and preceptors. In response to patients perceived as angry, rude, and uncooperative, students described themselves and their preceptors primarily as engaging in routine medical behaviours, followed by expressions of empathy. These encounters resulted in residual emotions as well as lessons learned. Fourth-year students reported more empathy, patient-centeredness, and patient ownership than third-year students. While student-physicians grew in professionalism and compassion, they also noted unresolved distressing emotions post-encounter. From third to fourth year, medical students undergo a process of professional growth that can be documented at a granular level through their perceptions of themselves, their patients, and their preceptors. Despite positive professional growth, students' lingering negative affect merits attention and support from clinical teachers.