The use of allograft bone is becoming increasingly common. The intrinsic mechanical and structural properties of the graft are of major importance for osseointegration. Current cleaning treatments using chemical or physical products increase biosafety but may disturb these bone characteristics. A new cleaning treatment for cancellous and cortical bone by simple mechanical washing (sonication and centrifugation) and supercritical carbon dioxide (scCO2) treatment was developed. The mechanical and structural properties of allografts cleaned with this treatment were compared with those obtained after preservation by freezing at −80°C. Three-point bending, compression and hardness tests were performed for biomechanical analysis. The structural characteristics of the allografts were evaluated by microscanner (histomorphometry) and scanning electron microscopy (surface analysis). All the data showed that the cleaned bone was generally stiffer owing to delipidation but its structure remained similar to that of the frozen bone. Bone cleaned by this new treatment thus displayed mechanical and structural properties close to those of frozen bone.