Background: This study focuses on furthering the understanding of doctoral researcher development, through the examination of significant events and application of the trajectories analysis framework. Conducting doctoral studies requires a high level of cognitive, personal and emotional competency. Students experience positive and negative emotions that affect their confidence and their performance, in both their doctoral studies and their personal life. Purpose: The aim of the study was to analyse, in depth, the emotional experiences of doctoral students when faced with different significant events throughout their doctoral studies and examine associations between their emotions and their trajectory. Methodology: A sub-sample of participants from a wider European study of 10 Spanish doctoral students was analysed. To delve into the emotional aspects of the PhD trajectories, a deeper analysis of three cases was carried out. A qualitative interpretative approach of a transversal nature was adopted to analyse, in detail, the type of events and the type of emotions associated along the students’ PhD trajectories. Findings: The analysis suggested that, despite the high negative emotions they felt, the participants valued the experiences lived throughout their doctorates and perceived them as mainly positive rather than negative. The most critical situations were linked to methodological and research design decisions that forced the participants to reassess their competencies and address the implications of these decisions in the final outputs of their research. The relationship with their supervisors was valued as crucial for their emotional well-being. The results highlight the relevance of the meaning-making process of the experience and the effect of previous emotions on how students interpret and cope with future events. Conclusions: Identifying specific issues that are emotionally significant and having a better understanding of the role of emotions experienced during the PhD can help to support and enable programme directors and supervisors to establish clearer monitoring and supervision strategies that promote reinforcement, personal validation, visibility of achievements and sustained motivation.