Inorganic–organic composite membranes (IOCMs) are an alternative separation method developed for their straightforward process, economic benefits, and ease of scaling up. The IOCMs in this study were prepared from a biopolymer chitosan matrix and rice husk-based silica filler to remove impurities from crude biodiesel. The IOCMs were prepared through phase inversions, in which the priorly prepared silica particles were dispersed in the dope solution of chitosan. The maximum loading of the silica particles was 60%, capable of reducing the soap level, free glycerol level, and acid number from 547.9 to 12.2 mg/L, 54 to 0.041%, and 2.02 to 1.12 mgKOH/g. These reduced impurity values have satisfied the standardized quality. The chemical composition and morphology of the IOCM was characterized using Fourier-transform infrared spectroscopy and scanning electron microscope–energy dispersive X-Ray spectroscopy. The IOCM water absorption-based porosity and swelling degree were studied as well. Further investigation using isothermal modeling revealed the adsorption dependency against the Sips model equation (R2 = 0.99 and root-mean-square errors = 1.77 × 10−8). Even though regeneration is still a challenging factor in this study, the IOCM prepared from chitosan and rice husk-derived silica particles could be used in crude biodiesel purification.