Abstract Membrane filtration and affinity-based adsorption are the two most used strategies in separation technologies. Here, µm-thick multifunctional and sustainable composite membranes of electrospun cellulose acetate (CA) infused with functionalized, anionic, and cationic cellulose nanocrystals (CNCs) with enhanced wettability, tensile strength, and excellent retention capacities were designed. CNCs could uniformly impregnate into the three-dimensional CA network to effectively improve its properties. The impregnation of cationic CNCs at 0.5 wt% concentration drastically increased the tensile strength (1669%) while maintaining high permeation flux of 9400 Lm-2h-1 which is remarkable with cellulose modified electrospun membranes. The membranes infused with anionic CNCs exhibited a particle retention efficiency of 96% for 500 nm and 77% for 100 nm latex beads whilst the cationic CNC membranes exhibited a combined particle retention strategy using selectivity and size exclusion with a retention of >81% with 100 nm latex beads and 80% with ∼50 nm silver nanoparticles. We envision that the developed multifunctional membranes can be utilized for affinity-based and size-exclusion filtration to selectively trap bacteria or substances of biological significance.