Cross-linking of magnetic nanoparticles with proteins plays a significant role in the preparation of new materials for biotechnological applications. The aim was the maximization of the magnetic mass attracted and protein loading of magnetic iron oxide nanoparticles coated with chitosan, synthesized in a single step by alkaline precipitation. Chitosan-coated magnetite particles (Fe3O4@Chitosan) were cross-linked to a xylanase and a cellulase (Fe3O4@Chitosan@Proteins), showing a 93% of the magnetic saturation of the magnetite. X-ray diffraction pattern in composites corresponds to magnetite. Thermogravimetry and differential scanning calorimetry showed that 162 mg of chitosan was coating one gram of composite and 12 mg of protein was cross-linked to each gram of magnetic support. Cross-linking between enzymes and Fe3O4@Chitosan was confirmed by infrared spectroscopy with Fourier transform, X-ray energy, and X-ray photoelectron spectroscopy dispersion analysis. From dynamic light scattering, transmission and electron microscopy the average particle size distribution was 230 nm and 430 nm for Fe3O4@Chitosan and Fe3O4@Chitosan@Proteins, showing agglomerates of individual spherical particles, with an average diameter of 8.5 nm and 10.8 nm, respectively. The preparation method plays a key role in determining the particle size and shape, size distribution, surface chemistry, and, therefore, the applications of the superparamagnetic nanoparticles.