The Mediterranean diet has been shown to improve cardiovascular health. Vegan diets have demonstrated similar benefits, albeit in fewer studies. In a comparative pilot study, we compared the effects of a short-term Mediterranean Diet (MD) and Vegan Diet (VD) on microvascular function and cholesterol levels in a healthy population. Twenty-four young (aged 18 to 35 years) healthy volunteers followed a four-week intervention (MD = 12; VD = 12) ad libitum. Pre and post-intervention anthropometrics, microvascular function (assessed via LDF and expressed as raw CVC and %CVC MAX), dietary-analysis data (Calories, Protein, Carbohydrates, Total Fat, Saturated Fat, Fibre), Mean Arterial Pressure (MAP), Blood Pressure, Total Cholesterol (TC), High Density Lipoprotein (HDL-C) and TC:HDL-C were compared. MD participants reduced Total Fat intake (p = 0.05). Saturated Fat decreased (MD: p = < 0.001; VD: p = 0.004) and Fibre increased (MD: p = 0.02; VD: p = < 0.001) in both groups. Dietary changes reflected improvements in plateau raw CVC in the MD group (p = 0.005), and a reduction in TC (p = 0.045) and weight loss (p = 0.047) in the VD group. The MD led to improvements in microvascular function; the VD led to reduced TC and weight loss. Although both diets might offer CVD risk-reduction benefits, evidence for the MD appeared to be stronger due to changes in vasodilatory ability and NO bioavailability.