Bone grafting is a common procedure for bone reconstruction in dentistry, orthopedics, and neurosurgery. A wide range of grafts are currently used, and xenografts are regarded as an interesting alternative to autogenous bone because all mammals share the same bone mineral component composition and morphology. Antigens must be eliminated from bone grafts derived from animal tissues in order to make them biocompatible. Moreover, the processing method must also safely inactivate and/or remove viruses or other potential infectious agents. This study assessed the efficacy of two steps applied in manufacturing some equine-derived xenografts: hydrogen-peroxide and e-beam sterilization treatments for inactivation and removal of viruses in equine bone granules (cortical and cancellous) and collagen and pericardium membranes. Viruses belonging to three different human viral species (Herpes simplex virus type 1, Coxsackievirus B1, and Influenzavirus type A H1N1) were selected and used to spike semi-processed biomaterials. For each viral species, the tissue culture infective dose (TCID50) on cell lines and the number of genome copies through qPCR were assessed. Both treatments were found to be effective at virus inactivation. Considering the model viruses studied, the application of hydrogen peroxide and e-beam irradiation could also be considered effective for processing bone tissue of human origin.