Functionalization and post-synthetic modification (PSM) of metal-organic frameworks (MOFs) are two important routes to obtain MOFs with full potential in mixed matrix membrane (MMM) fabrication. We synthesized UiO-66 and two derivatives UiO-66-NH2 and UiO-66-NH-COCH3 with less than 50 nm particle size. The CO2 uptakes at 10 bar in the two functionalized UiO-66s were improved by 44% and 58%, respectively, with respect to the pristine solid. The MOF nanoparticles were incorporated into the highly permeable polymer 6FDA-DAM, making MMMs with 5–24 wt% particle loadings. All fillers and membranes were characterized accordingly, and their gas separation performances were evaluated by feeding CO2/CH4 equimolar mixtures at 2 bar pressure difference at 35 °C. CO2 permeability (PCO2) of pristine 6FDA-DAM (PCO2 = 997 ± 48 Barrer, αCO2/CH4 = 29 ± 3) increased by 92% with 20 wt% UiO-66 loading, while maintaining the CO2/CH4 selectivity. Improvements of 23% and 27% were observed for PCO2 with the same 20 wt% loading of UiO-66-NH2 and UiO-66-NH-COCH3, respectively. The αCO2/CH4 was improved up to 16% using both functionalized UiO-66 type MOFs. The best separation performance in this work was obtained with 14 wt% UiO-66 MMM (PCO2 = 1912 ± 115 Barrer, αCO2/CH4 = 31 ± 1), 16 wt% UiO-66-NH2 MMM (PCO2 = 1223 ± 23 Barrer, αCO2/CH4 = 30 ± 1) and 16 wt% UiO-66-NH-COCH3 MMM (PCO2 = 1263 ± 42 Barrer, αCO2/CH4 = 33 ± 1) at 2 bar feed pressure difference. The measurement was also conducted with various binary compositions (CO2 = 10 – 90%), both at low and high pressures up to 40 bar at 35 °C, showing no pressure-related CO2-induced plasticization. The atomistic modelling for the MOF/polymer interface was consistent with a moderate MOF surface coverage by 6FDA-DAM which did not play a detrimental role in the membrane performance.