The present disclosure provides methods for functionalizing the surfaces of cellulose nanoparticles. In embodiments, nanoparticles are aerosolized, and then passed through a flow reactor where they are contacted with gaseous reactants to functionalize the surface of the nanoparticles. In other embodiments, the nanoparticles are aerosolized, and then passed through a plasma reactor where they are contacted with gaseous reactants to functionalize the surface of the nanoparticles. Once the functionalized nanoparticles are produced, they may be combined with polymers to form polymer composites having both a polymer and the functionalized nanoparticles. Systems for producing these functionalized nanoparticles, coupled with downstream polymer processing equipment for forming the polymer composites, are also provided.