Allograft bone tissue has a long history of use. There are two main ways of preserving allografts: by cold (freezing), or at room temperature after an additional cleaning treatment using chemicals. These chemicals are considered potentially harmful to humans. The aim of the study was (i) to assess the presence of chemical residues on processed bone allografts and (ii) to compare the in vitro biocompatibility of such allografts with that of frozen allografts. The presence of chemical residues on industrially chemically treated bone was assessed by high performance liquid chromatography (HPLC) after extraction. Biocompatibility analysis was performed on primary osteoblast cultures from Wistar rats grown on bone disks, either frozen (F-bone group) or treated with supercritical carbon dioxide with no added chemical (scCO2-bone group) or industrially treated with chemicals (CT-bone group). Cell viability (XTT) was measured after one week of culture. Osteoblastic differentiation was assessed after 1, 7 and 14 days of culture by measuring alkaline phosphatase (ALP) activity directly on the bone discs and indirectly on the cell mat in the vicinity of the bone discs. Residues of all the chemicals used were found in the CT-bone group. There was no significant difference in cell viability between the three bone groups. Direct and indirect ALP activities were significantly lower (−40% to −80%) in the CT-bone group after 7 and 14 days of culture ( p < 0.05). Residues of chemical substances used in the cleaning of bone allografts cause an in vitro decrease in their biocompatibility. Tissue cleaning processes must be developed that limit or replace these chemicals to favor biocompatibility.