The human plasma proteome is rather well studied, but not that of other species, including horses. The aims of this study were to (1), explore differences in plasma proteomic profile of young elite harness trotters kept under standardised conditions and subjected to two different training programmes for 2 years and (2) explore changes in proteomic profile over time during the training period. From September at age 1.5 year to March at age 2 years, 16 Standardbred horses were exposed to the same training programme. In March, high-intensity training was introduced and the horses were divided into two training groups (High and Low). Blood samples were collected at rest in December as 1.5-year-olds, July as 2-year-olds, December as 2.5-year-olds and December as 3.5-year-olds. Untargeted proteomics was performed and a hypothesis-generating approach was used in statistical analysis (t-tests). At the age of 2.5 years, the level of serotransferrin was higher in the High group (P = 0.01) and at least at one sampling occasion, proteins associated with fat metabolism, oxidant/antioxidant processes, cardiovascular responses, bone formation and inflammation were lower in High group compared to Low (P < 0.05). Analyses of changes over time revealed that levels of proteins involved in energy metabolism, red cell metabolism, circulation, oxidant/antioxidant activity, bone formation, inflammation, immune modulation and cellular and vascular damage changed (P < 0.05). The results indicate that proteomics analysis of blood plasma could be a viable tool for evaluation of exercise adaptations, performance and for health monitoring, with several potential biomarkers identified in this study.