The integration of nanoporous membranes into microfluidic devices allows a wide range of analytical and biochemical applications such as stable concentration gradient generation, sample pre-concentration, and ion and biomolecule filtration in a controllable manner. However, further applications of nanoporous membranes in microfluidic devices require rapid and controllable fabrication methods of various nanoporous precursor materials; currently, few such methods exist. Here, we describe simple and robust methods that can be used for microfabricating four different precursor materials as leakage-tight membranes in a microfluidic channel network. The methods consist of a common integration process and individual solidification processes such as solvent evaporation, UV-curing, and temperature treatment. We demonstrate that the fabricated membranes can be used for electrokinetic, nanofluidic pre-concentration of bio-samples such as proteins, cells, and microspheres on either the anodic or cathodic side of the membranes. In addition, we not only characterize the physicochemical properties of the membranes such as conductance of membrane-integrated microchannels, relative permselectivity, and pre-concentration ability, but also compare fabrication availability, membrane robustness, surface charge density tunability and biocompatibility with buffer solutions. The methods are versatile for many nanoporous precursor materials and easy to control the location and dimension of the membranes. Hence, the methods developed and the characterized properties of the membranes tested in this work could be widely employed for further applications of nanoporous membranes in microfluidic systems.