Aim of the study The aims of this investigation were: (1) to calculate baseline prevalence of FES patients with relevant depressed mood (DM), (2) to longitudinally monitor DM levels over a 12-month follow-up, and (3) to investigate their associations with clinical data and the specific treatment components of an “Early Intervention in Psychosis” (EIP) program. Subject or material and methods The Positive And Negative Syndrome Scale (PANSS) was completed by all FES participant. Individuals with a baseline PANSS “Depression” item subscore of ≥ 5 were classified as having relevant depressed mood (FES/DM+). Chi-square and Mann-Whitney tests were used for inter-group comparisons. A linear regression analysis was also performed. Results Fifty-three (33.3%) participants were in the FES/DM+ subgroup. Relevant baseline DM at baseline was associated with female gender and a higher PANSS “Positive Symptoms” score. Across the follow-up, FES individuals improved their DM levels. This was significantly related to a longitudinal decrease in PANSS “Positive Symptoms” levels. Discussion More than 1/3 of FES subjects had relevant DM already at the recruitment time in an EIP service. This suggests that relevant depression in FES subjects is usually under-treated. Moreover, we observed a significant decrease in DM severity levels across the follow-up. This decrease was associated with the longitudinal severity reduction in positive symptom levels, reflecting their state-related fluctuations. Conclusions DM is relatively frequent in FES, already at the recruitment in EIP services. However, its severity decreases overtime within specialized EIP programs.