A novel method for the rapid magnetic separation of wine yeast cells from sparkling wine was developed. The cells were made responsive to a magnetic field by the absorption of superparamagnetic nanoparticles of iron oxide maghemite (γ-Fe 2 O 3 ) coated with a thin layer of silica and grafted with (aminoethylamino)propylmethyldimethoxysilane (APMS). The terminal amino groups of the APMS molecules provide a positive charge on the nanoparticles’ surfaces and promote their electrostatic absorption onto the negatively charged surfaces of the cells. The optimal mass ratio between the magnetic nanoparticles and the wine yeast was determined to be 1:10. The separation of the “magnetized” biomass in the magnetic field as well as the influence of the magnetic nanoparticles on the yeast metabolism was studied. Scanning and transmission electron microscopy showed that the magnetic nanoparticles remained fixed at the microbial cell surfaces, even after fermentation. The results of the chemical analysis demonstrated that besides the faster microbial kinetics there were no negative influences on the cell metabolism. The same results were confirmed in sensorial analyses of the sparkling wine. The separation of the magnetized waste biomass in the bottle neck using relatively weak magnetic-field gradient can be successfully completed in approximately 15 min.