This work aims to characterize the serum profile of athletes after the administration of ecdysteroids, natural steroid hormones recently reported to enhance athletic performance. The combination of mass spectrometry and chemometric tools may allow to differentiate physiological effects from post‐training and intake‐driven effects. Serum samples were collected from 46 healthy male volunteers and divided into four groups: control (two capsules/day of Peak Ecdysone without training), placebo (two capsules without ecdysteroids with training), Ec1 (two capsules/day Peak Ecdysone with training), and Ec2 (eight capsules/day Peak Ecdysone with training). Metabolic profiling was measured using a SCIEX Triple Quadrupole LC‐MS/MS system coupled with the Biocrates AbsoluteIDQ p180 kit, which allows quantitation of a large panel of metabolites that were subjected to multivariate analysis. Unsupervised analysis of the data found no significant differences between the placebo and the ecdysteroid supplementation groups. By merging Ec1 and Ec2 into a single group, coded as treated, a clear discrimination between the control and placebo groups was observed. Phosphatidylcholines were among the most significant features of ecdysteroids administration, showing a dose‐dependent effect in Ec1 and Ec2 groups. As specific metabolic phenotypes can result from years of training, the discrimination of physiological effects from those caused by the administration of banned substances can be a valuable analytical strategy for the interpretation of adverse analytical findings in the anti‐doping field.