This study aims to determine the effects of essential oils of Origanum dubium (DUB), Origanum vulgare subsp. hirtum (HIR), and Lavandula angustifolia (LAV) on lipid profiles and liver biomarkers in athletes. Thirty-four trained athletes were randomly assigned to one of three experimental groups or the control group (CON). The concentrations of serum lipids and liver biomarkers were assessed before and after the 14-day essential oil intervention. Gas chromatography-mass spectrometry analysis showed 68.0 and 82.1% carvacrol in DUB and HIR, respectively, and 34.50% linalyl acetate and 33.68% linalool in LAV essential oils. One-way analysis of covariance (ANCOVA) indicated a significant difference (p = 0.001) among the groups for high-density lipoprotein cholesterol (HDL-C) when the associated preintervention values were used as a covariate. The related pairwise comparisons revealed that DUB (p = 0.001) and HIR (p = 0.024) had greater HDL-C values than CON. From the two-way ANOVA, an interaction between time (before vs. after) and the groups (DUB vs. HIR vs. LAV vs. CON) was found for HDL-C (p = 0.030). Findings indicated a significant increase in DUB (p = 0.0001) and HIR (p = 0.010) for HDL-C, and there was a significant decrease in DUB (p = 0.023) for low-density lipoprotein cholesterol. However, there was no difference in total cholesterol, triglycerides, and all liver biomarkers.