The study investigated whether bicycle compared with car commuting, over relatively small distances, has positive effects on physiological variables, cardiometabolic fitness and CO2 output in the atmosphere. Bike Commuters (11 M, 15 F; age [median value (interquartile range)] 51.5 (38.3–56.8) years; body mass index [BMI] 22.8 (21.0–24.1) kg m−2) were compared with Car Commuters (12 M, 19 F; age 47.0 (36.0–56.5) years; BMI 23.5 (21.4–24.9) kg m−2). In a longitudinal arm of the study, 20 Car Commuters were re-evaluated after they switched for 24 weeks to bicycle commuting (Car→Bike Commuters). Measurements included peak aerobic power () and ventilatory thresholds on a cycle ergometer, blood flow increase in the common femoral artery during a passive leg movement (PLM) test, energy expenditure and exhaled during commuting. Bike Commuters had higher (33.7 (31.3–38.1) versus 25.3 (23.5–28.9) mL kg−1 min−1, P textless 0.001) and ventilatory thresholds than Car Commuters, higher Δpeak blood flow (+25%, P = 0.04) and area under the blood flow versus time curve (+46%, P = 0.03) during PLM, and an enhanced skeletal muscle oxidative metabolism. and PLM variables increased in Car→Bike Commuters. Metabolic CO2 output during bicycle commuting was ∼12 times less than that for a petrol car. In moderately active individuals, short-distance bicycle commuting at moderate intensity was associated, compared with car commuting, with positive effects on several physiological functions and environmental factors.