Methods of decontaminating bone tissue and an apparatus or system for the same are provided. The methods can be multi-batch processes and include contacting the bone tissue having contaminants with carbon dioxide to decontaminate the bone tissue and to form carbon dioxide having contaminants. The contaminated carbon dioxide is collected and the contaminants are removed to obtain purified carbon dioxide which can be recycled to treat contaminated bone tissue. The contaminated carbon dioxide can be purified by bubbling it through water and/or an organic solvent followed by acid treatment, filtering and liquefying the carbon dioxide. Contaminants that can be removed from contaminated bone tissue, and in turn, from contaminated carbon dioxide include infectious organisms, bacteria, viruses, protozoa, parasites, fungi and mold or a mixture thereof.
