Magnetic cellulose beads synthesized either from cotton or Avicel were applied to the immobilization and purification of secreted Aspergillus niger proteins involved in alfalfa biomass degradation. Immobilized proteins were subjected to trypsin digestion and data-dependent acquisition LC-MS/MS was performed to identify the proteins bound to the beads. The techniques developed were effective not only for clarified and concentrated culture supernatants, but also for untreated samples containing biomass and fungal mycelia, as well as the resuspended pellet fraction. Proteins identified included cellulases with a fungal-type cellulose-binding domain, other glycoside hydrolases without conserved or obvious cellulose binding modules and some proteins associated with hydrophobic surface interactions. These studies will be expanded to include other species of fungi and sources of biomass.