Unilateral physical training can enhance muscular size and function as well as vascular function in the trained limb. In non-athletes, the preferred arm for use during unilateral tasks may exhibit greater muscular strength compared to the non-preferred arm. It is unclear if lower limb preference affects lower limb vascular function or muscular endurance and power in recreationally active adults. To examine the effect of lower limb preference on quadriceps muscle size and function and on lower limb vascular function in middle-aged adults. Twenty (13 men, 7 women) recreationally-active middle-aged (55 ± 7 yrs) adults underwent measurements of quadriceps muscle thickness, strength, mean power, endurance, and arterial stiffness, calf venous compliance, and calf blood flow in the preferred and non-preferred lower limb. The preferred limb exhibited greater calf vascular conductance (31.6 ± 15.5 versus 25.8 ± 13.0 units flow/mmHg; p = 0.011) compared to the non-preferred limb. The interlimb difference in calf vascular conductance was negatively related to weekly aerobic activity (hrs/week) (r = −0.521; p = 0.019). Lower limb preference affects calf blood flow but not quadriceps muscle size or function. Studies involving unilateral lower limb testing procedures in middle-aged individuals should consider standardizing the testing to either the preferred or non-preferred limb rather than the right or left limb.