Magnetic photonic crystals are an emerging class of responsive colloidal systems with unique variable optical properties. This article is dedicated to the first example of polyelectrolyte-based magnetic photonic crystals produced by layer-by-layer adsorption of polymeric molecules onto magnetite cores. Proper selection of the polycationic and polyanionic molecules allowed to produce a stable colloidal system composed of monodisperse nanoaggregates with a mean diameter of 180 nm. In the presence of weak magnetic fields up to 650 G, the reflectance spectra of the colloid system showed a blue shift, changing spectra peak maximum from 720 to 445 nm. Mild synthetic conditions allowed to use natural polymers, such as heparin, expanding the bioactivity of the produced material. Magnetic photonic crystals have demonstrated excellent biocompatibility with minor cytotoxicity on HeLa cell line up to 200 μg/mL concentration, and anticoagulant activity comparable to free heparin. The synthesized material can find its application in the fields of optics, biosensorics, or biocompatible magnetic drug delivery systems for anticoagulant therapy.