Thin‐film SAPO‐34 membranes can separate CO2 efficiently. However, crack formation due to thermal expansion mismatch between the SAPO‐34 crystals and the support occurs at high operating temperatures, thereby resulting in a dramatic loss. Nanocomposite architecture SAPO‐34 membranes prepared via pore‐plugging hydrothermal synthesis could overcome this problem. In this study, nanocomposite SAPO‐34 membranes were synthesized via pore‐plugging hydrothermal and evaluated for N2/CO2 separation. Physico‐chemical property of the as‐synthesized membranes was checked with X‐ray diffraction, scanning electron microscope, thermal gravimetric analyser, and Fourier transform infrared. The X‐ray diffraction pattern reveals characteristic peaks associated with the rhombohedral crystal type of SAPO‐34; thermal gravimetric analyser shows a high thermal stability, Fourier transform infrared spectra indicate the presence of the D6R and T–O vibrations which form an essential part of the SAPO‐34 structure, and scanning electron microscope images of the membranes reveal cubic morphology of the SAPO‐34 crystals embedded in the ceramic support. Single gas permeation experiments using pure component of CO2 and N2 conducted to evaluate the separation performance of the membranes during post‐combustion CO2 capture reveal that ideal selectivity increased significantly for multistage pore‐plugging hydrothermal synthesis. The Maxwell–Stefan model describes adequately the CO2 permeation behaviour through the membrane as well. However, the membrane flux reduced owing to increase in membrane thickness. © 2017 Curtin University and John Wiley & Sons, Ltd.