Overweight and obesity in horses affect their athletic performance negatively, making it therefore necessary to develop training protocols that reduce their body fat without causing hoof injuries. The objective of the study was to describe the effect of the application of a swimming training program on metabolic and endocrine variables, in addition to evaluating the changes in subcutaneous fat thickness (SFT) in a group of overweight Colombian Paso Horses (CPHs). Six CPHs were subjected to a decreasing intensity swimming program for four months. The effect of this training on metabolic variables (i.e. aspartate aminotransferase, creatine kinase, triglycerides, cholesterol, glucose) and endocrines (cortisol and insulin) was studied every two months. Additionally, changes in the neck, lumbar, and gluteal SFTs were evaluated. The information was analysed using descriptive statistics, in addition to repeated measures analysis of variance for non-parametric data in the three training moments (P<0.1) and correlation analysis between the SFT and the metabolic and endocrine variables of interest. The swimming training program for CPHs tested in this study produced more evident redistribution of adipose tissue in the gluteal region (Initial SFT = 5.2±2.08 mm; Final SFT = 3.45±2.8 mm), conversion of body mass without weight modification, and use of energy sources such as triglycerides and increased sensitivity to insulin. A limitation of the study was that the horses were not selected according to age, nor were control animals used. In addition, the limited number of horses makes extrapolation of the results inappropriate. In conclusion, the swimming training program with decreasing intensity carried out over a four-month period modified body adipose tissue in CPHs, promoting the use of energy sources, such as triglycerides and increased insulin sensitivity.