In this study, polyacrylonitrile nanofiltration membranes containing two Fe-based nanoparticles were fabricated through phase inversion method by incorporation of goethite (Goe) and maleate ferroxane (Mf), separately in casting solutions. Goe and Mf nanoparticles were first synthesized and characterized by scanning electron microscopy (SEM), Fourier Transform Infrared (FTIR) spectrometer, and X-ray diffraction (XRD) analyses. The synthesized membranes were characterized by SEM, FTIR-attenuated total reflectance (FTIR-ATR), atomic force microscopy (AFM), water contact angle (CA), and porosity measurements. The nanofiltration performance of membranes was studied by investigation of dye removal. Composite membranes showed better dye retention as compared with pristine PAN due to the higher repulsive force between dye and nanocomposite membrane functional groups. The presence of nanoparticles in the PAN membranes decreased CA, increased permeated water flux (PWF), and bulk water affinity (BWA). The reason of these changes was improvement in the surface hydrophilicity and decreasing the surface roughness. The addition of nanoparticles resulted in reduction of fouling phenomenon. Composite membranes had higher reversible fouling and flux recovery ratio (FRR) than bare membranes. In addition, the results displayed that the 0.5 wt% Mf membrane had the best performance among other membranes. FTIR-ATR analysis demonstrated the stability of nanoparticles after three times of dye rejection. Also, the membranes retained the acceptable performance after four cycles of powder milk fouling tests.