OBJECTIVE: The PREDIMED trial showed that Mediterranean diets supplemented with either extra-virgin olive oil or nuts reduced incident cardiovascular events compared to a control diet. Consumption of both supplemental foods has been associated with reduced LDL-cholesterol, but it is unknown whether they can shift lipoprotein subfractions to a less atherogenic pattern. We investigated changes in adiposity and lipoprotein subfractions after consumption of the PREDIMED diets. METHODS: In a PREDIMED sub-cohort (n = 169), lipoprotein subclasses (particle concentrations and size) were determined by nuclear magnetic resonance spectroscopy at baseline and after intervention for 1 year. RESULTS: Participants allocated to the Mediterranean diet supplemented with nuts showed significant reductions from baseline of waist circumference (mean [95% CI]; -5 cm [-7; -3]) and concentrations of medium-small (-27 nmol/l [-46; -8]) and very small LDL (-111 nmol/l [-180; -42]); decreased LDL particle number (a nuclear magnetic resonance-specific measurement) (-98 nmol/l [-184; -11]); and an increase of large LDL concentrations (54 nmol/l [18; 90]), with a net increase (0.2 nmol/l [0.1; 0.4]) of LDL size. The Mediterranean diets with olive oil and nuts increased large HDL concentrations (0.6 μM [0.0; 1.1] and 1.0 μM [0.4; 1.5], respectively). Compared to the other two intervention groups, participants in the nut-enriched diet showed significantly reduced waist circumference (p ≤ 0.006, both) and increased LDL size (p < 0.05, both). CONCLUSION: Lipoprotein subfractions are shifted to a less atherogenic pattern by consumption of Mediterranean diets enriched with nuts. The results contribute mechanistic evidence for the reduction of cardiovascular events observed in the PREDIMED trial.