We introduce highly antifouling Polymer-Nanoparticle-Nanoparticle/Polymer (PNNP) hybrid membranes as multi-functional materials for versatile purification of wastewater. Nitrogen-rich polyethylenimine (PEI)-functionalized halloysite nanotube (HNT-SiO2-PEI) nanoparticles were developed and embedded in polyvinyl chloride (PVC) membranes for protein and dye filtration. Bulk and surface characteristics of the resulting HNT-SiO2-PEI nanocomposites were determined using Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), and thermogravimetric analysis (TGA). Moreover, microstructure and physicochemical properties of HNT-SiO2-PEI/PVC membranes were investigated by scanning electron microscopy (SEM), atomic force microscopy (AFM), and attenuated total reflectance (ATR)-FTIR. Results of these analyses indicated that the overall porosity and mean pore size of nanocomposite membranes were enhanced, but the surface roughness was reduced. Additionally, surface hydrophilicity and flexibility of the original PVC membranes were significantly improved by incorporating HNT-SiO2-PEI nanoparticles. Based on pure water permeability and bovine serum albumin (BSA)/dye rejection tests, the highest nanoparticle-embedded membrane performance was observed at 2 weight percent (wt%) of HNT-SiO2-PEI. The nanocomposite incorporation in the PVC membranes further improved its antifouling performance and flux recovery ratio (96.8%). Notably, dye separation performance increased up to 99.97%. Overall, hydrophobic PVC membranes were successfully modified by incorporating HNT-SiO2-PEI nanomaterial and better-quality wastewater treatment performance was obtained.