Reducing sedentary behaviour changes serum lipid and lipoprotein concentrations. However, detailed insights into effects on lipid and lipoprotein subclasses and functionalities, and markers of inflammation and endothelial dysfunction are lacking. In this randomised cross-over study, 24 sedentary overweight/obese individuals followed two 4-day activity regimens under free-living conditions. The "Sit" regimen involved 13.5 h/day sitting, 1.4 h/day standing, and 0.7 h/day self-perceived light-intensity walking. During the "SitLess" regimen these activities lasted respectively 7.6, 4.0, and 4.3 h/day. Blood samples collected after each regimen were analysed for markers of lipid and lipoprotein metabolism, inflammation, and endothelial dysfunction. Compared to the Sit regimen, SitLess increased serum cholesterol concentrations in HDL (0.06 mmol/l, p = 0.002), large HDL A (0.05 mmol/l, p < 0.001), medium HDL B (0.02 mmol/l, p < 0.001) and small HDL C (0.09 mmol/l, p < 0.001), LHDL particles concentrations (999 nmol/l, p < 0.001) and HDL size (0.2 nm, p < 0.001). ApoA-I, pro-ApoA-I, and HDL functionality remained unchanged. Triglyceride (-0.49 mmol/l, p < 0.001), ApoB100 (-0.68 g/l, p = 0.007), and particle concentrations of LVLDL (-2.2 nmol/l, p = 0.002), SLDL (-58 nmol/l, p = 0.024) and LDL (-86 nmol/l, p = 0.006) decreased. Cholesterol concentrations in VLDL (-0.15 mmol/l, p < 0.001), IDL (-0.11 mmol/l, p = 0.001) and small LDL C (-0.04 mmol/l, p < 0.001) decreased, while large LDL A cholesterol (0.07 mmol/l, p = 0.031) and LDL particle size (0.1 nm, p = 0.004) increased. CRP concentrations (0.95 mg/dl, p = 0.003) rose. Substituting sitting with standing and self-perceived light walking in free-living conditions, translates into lower CVD risk lipid and lipoprotein profiles in individuals who are overweight/obese. CRP significantly increased after the SitLess regimen.