The effect of the morphology and content of zinc oxide nanoparticles (ZnO-NPs) on the physicochemical, mechanical, and gas transport properties of the polyurethane (PU) mixed matrix membranes (MMMs) with respect to CO2 recovery from CH4, O2, and N2 was studied. The MMMs based on PU with spherical and rod-shaped ZnO-NPs at various loadings, namely, 0.05, 0.1, 0.5, 1, and 2 wt. %, were prepared with membrane density control and studied using AFM, wettability measurements, surface free energy calculation, gas separation and mechanical testing. To evaluate the resistance of the ZnO-NPs to agglomeration in the polymer solutions, zeta potential was determined. The ZnO-NPs with average cross sectional size of 30 nm were obtained by plasma-enhanced chemical vapor deposition (PECVD) from elemental high-purity zinc in a zinc-oxygen-hydrogen plasma-forming gas mixture. It was established that the spherical ZnO-NPs are promising to improve the gas performance of PU-based MMMs for CO2 recovery from natural gas, while the rod-shaped NPs better demonstrate their potential in capturing CO2 in flue gases.