Cross-sectional research has shown that clinical psychology trainees usually face a wide range of stressors related to the clinical practice and tend to present higher distress than other psychology students. However, to our knowledge, no longitudinal study has been conducted analysing this fact. Specifically, this study analyses the evolution of emotional symptoms among a group of novice clinical psychology trainees compared with a control cohort. We recruited 575 Colombian Psychology undergraduates: 52.9% were in the semester in which they began their clinical practice, and 47.1% were attending a regular semester. At the beginning of the semester (T1), participants responded to measures of emotional symptoms (Depression, Anxiety, and Stress Scale-21, DASS-21; General Health Questionnaire-12, GHQ-12). Approximately two months later (T2), participants responded to the DASS-21 and GHQ-12. The two groups did not differ in their scores on the DASS-21 and the GHQ-12 at T1. Bayesian repeated-measures ANOVA showed that clinical psychology trainees showed higher increases in scores on the DASS-Total, DASS-Depression, and DASS-Stress than participants attending a regular semester. This is the first study that shows clinical psychology trainees experiencing a higher increase in emotional symptoms compared with a control cohort.