In-tissue embedded magnetic nanoparticle (MNPs) detection is one of the most interesting cases for cancer research. In order to understand the origin, the limits and the way of improvement of magnetic biosensor sensitivity for the detection of 3D mezoscopic distributions of MNPs, we have developed a magnetoimpedance biosensor prototype with a Cu (3 nm)/FeNi(100 nm)5/Cu(500 nm)/FeNi(100 nm)/Cu(3 nm)5 rectangular sensitive element. Magnetoimpedance (MI) responses were measured with and without polyacrylamide ferrogel layer mimicking natural tissue in order to evaluate stray fields of embedded MNPs of γ-Fe2O3 iron oxide. A model for MI response based on a solution of Maxwell equations with Landau-Lifshitz equation was developed in order to understand the origin of the prototype sensitivity which reached 1.3% of ΔZ/Z per 1% of MNPs concentration by weight. To make this promising technique useful for magnetically labeled tissue detection, a synthesis of composite gels with MNPs agglomerates compactly located inside pure gel and their MI testing are still necessary. •Magnetoimpedance (MI) biosensor prototype with Cu/FeNi5/Cu/FeNi/Cu5 element was designed and tested.•MI responses were measured with and without ferrogel layer mimicking natural tissue.•We were able to evaluate stray fields of 3D distributions of embedded magnetic nanoparticles.•Electromagnetic MI model was developed in order to understand the 1.3% of ΔZ/Z per 1 wt% of MNPs concentration prototype sensitivity.