Scope: To assess whether following a Mediterranean diet (MedDiet) improves atherothrombosis biomarkers in high cardiovascular risk individuals. Methods and results: In 358 random volunteers from the PREvención con DIeta MEDiterránea trial, the 1-year effects on atherothrombosis markers of an intervention with MedDiet, enriched with virgin olive oil (MedDiet-VOO; n = 120) or nuts (MedDiet-Nuts; n = 119) versus a low-fat control diet (n = 119), and whether large increments in MedDiet adherence (≥3 score points, versus compliance decreases) and intake changes in key food items are associated with 1-year differences in biomarkers. Differences are observed between 1-year changes in the MedDiet-VOO intervention and control diet on the activity of platelet activating factor acetylhydrolase in high-density lipoproteins (HDLs) (+7.5% [95% confidence interval: 0.17; 14.8]) and HDL-bound 1-antitrypsin levels (−6.1% [−11.8; −0.29]), and between the MedDiet-Nuts intervention and the control arm on non-esterified fatty acid concentrations (−9.3% [−18.1; −0.53]). Large MedDiet adherence increments are associated with less fibrinogen (−9.5% [−18.3; −0.60]) and non-esterified fatty acid concentrations (−16.7% [−31.7; −1.74]). Increases in nut, fruit, vegetable, and fatty fish consumption, and decreases in processed meat intake are linked to enhancements in biomarkers. Conclusion: MedDiet improves atherothrombosis biomarkers in high cardiovascular risk individuals.