Prevention of cardiovascular (CV) disease is considered a central issue in public health and great attention is payed to nutritional approaches, including consumption of functional foods to reduce CV risk in individuals without indications for anti-atherosclerotic drugs. Cholesterol efflux capacity (CEC) is an important anti-atherogenic property of HDL and a marker of CV risk. We evaluated the effect of a daily consumption of an innovative whole-wheat synbiotic pasta, compared to a control whole-wheat pasta, on serum ATP binding cassette G1 (ABCG1)-mediated CEC in healthy overweight or obese individuals. Study participants (n = 41) were randomly allocated to either innovative or control pasta, consumed daily for twelve weeks. Serum CEC was measured before and after the dietary intervention, by a well-established radioisotopic technique on Chinese Hamster Ovary Cells transfected with human ABCG1. The innovative synbiotic pasta consumption was associated to a significantly higher post treatment/baseline ratio of ABCG1-mediated CEC values with respect to control pasta (mean ratio 1.05 ± 0.037 and 0.95 ± 0.042 respectively, p < 0.05). Analysis of the relationship between ABCG1-mediated CEC and glycemia, homocysteine, total folates and interleukin-6 showed specific changes in the correlations between HDL function and glycemia, oxidative and inflammatory markers only after synbiotic pasta consumption. This is the first report on serum CEC improvement obtained by a new synbiotic functional pasta consumption, in absence of lipid profile modifications, in overweight/obese participants. This pilot study suggests that a simple dietary intervention can be a promising approach to CV preservation through improving of athero-protective HDL function.