Magnetite (Fe 3 O 4 ) and magnetic core‐shell mesoporous silica (Fe 3 O 4 ‐mSiO 2 ) nanoparticles are employed to coat cotton fibers using a room temperature water‐based direct electrostatic assembly method with polyelectrolytes. Core‐shell nanoparticles are fabricated by coating super‐paramagnetic magnetite clusters with a mesoporous silica layer (mSiO 2 ) using a surfactant‐templating approach. The Fe 3 O 4 clusters are initially synthesized by a co‐precipitation process. The cotton fibers are modified through a layer‐by‐layer technique using dipping cycles with PDDA and PSS polyelectrolytes solutions to enable further nanoparticles attachment. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) images provides morphologic information of the synthesized nanoparticles and the modified cotton fibers. Composition and physicochemical properties are studied by powder XRD, FTIR, and SEM‐EDX methods, and thermogravimetric analysis (TGA) are carried out to determine the amount of nanoparticles adsorbed onto cotton samples. The saturation magnetization (M S ) of nanoparticles determined by a vibrating sample magnetometer (VSM) is greater than that of the cotton‐nanoparticles nano‐composites. Potential applications of these composite materials can include protective clothing and transdermal drug delivery systems.