This work reports the assembly of mesoporous iron oxide nanoparticles (meso‐MNPs) with cryogel scaffolds composed of chitosan and gelatin. Meso‐MNPs with a particle size ranging from 2 and 50 nm, a surface area of 140.52 m2 g−1, and a pore volume of 0.27 cm3 g−1 were synthesized on a porous SiO2 template in the presence of PEG 6000 followed by leaching of SiO2. Different ratios of meso‐MNPs were successfully incorporated into chitosan:gelatin cryogels up to an amount equivalent to the entire amount of polymer. The morphological structure and physicochemical properties of the cryogels were directly affected by the amount of MNPs. VSM curves showed that all composite cryogels could be magnetized by applying a magnetic field. In the context of the safety of magnetic cryogel scaffolds for use in biomedicine, it is important to note that all values are below the exposure limit for static magnetic fields, and according to cytotoxicity data, scaffolds containing meso‐MNPs showed nontoxicity with cell viability ranging from 150% to 275%. In addition, microbial analysis with gram‐negative and gram‐positive bacteria showed that the scaffolds exhibited activity against these bacteria.