This work focuses on the obtention of magnetic nanoparticles functionalised with heparin (MNPH) and their interaction with Aspergillus niger lipase enzyme. The MNPH were obtained by the coprecipitation method, its characterisation was carried out by Fourier transform infrared spectroscopy, X-ray diffraction, and alternating gradient magnetometry. Functionalisation with heparin was carried out by ultrasound at various times, later the absorption of the enzyme was carried out with two temperatures 4 and 25°C at different concentrations of lipase. For the recovery of the enzyme, a Plackett-Burman design was used, which indicates that the recovered lipase maintains its enzymatic activity when the ionic strength is lower, it was characterised by sodium dodecyl sulphate-page with which it is demonstrated that it is possible to recover the lipase enzyme through the designed nanostructured system.