The Magneto-photonic crystals/MPCs are promising candidates for devising high-fidelity embedded biosensor systems which offer facile & real time detection of diagnostic proteins. Despite extensive use of magnetic nanomaterials for theranostic applications, the idea of exploiting its photonic response when assembled as a colloid inside a matrix remains unexplored. Herein, we report a novel label free method for quantitative detection of interleukin 6 which is a widely used prognostic marker for multiple pathological conditions. Cobalt ferrite/CoF and magnetite nanoparticles with Ms of 74.8 and 77 emu g−1 were assembled inside a hydrogel matrix with the application of an external magnetic field. Through the use of click chemistry, detecting antibodies were immobilized on their surface. The interaction of interleukin 6 with the antibodies produces a blue- shift in resonant wavelength and the reflectance intensity increases up to 50% and 44% when tested with CoF & magnetite based MPC respectively at a concentration of 50 pg ml−1. The dynamic range of the sensor lies within the prognostic values of IL-6, and the integrated sensing mechanism proposed in this study provides an ideal platform for real-time management of sepsis in patients with higher degree burns.