Recombinant proteins and other materials of industrial interest produced in Escherichia coli are usually retained within the bacterial cell, in the cytoplasmic space, where they have been produced. Different protocols for cell disruption have been implemented as an initial downstream step, which keeps the biological and mechanical properties of the process products. Being necessarily mild, these approaches often result in 95-99% cell disruption, what is more than acceptable from the yield point of view. However, when the bacterial product are nano or microparticulate entities that tend to co-sediment with entire bacterial cells, the remaining undisrupted bacteria appear as abounding contaminants, making the product not suitable for a spectrum of biomedical applications. Since bacterial inclusion bodies are now seen as bacterial materials valuable in different fields, we have developed an alternative cell disruption protocol that permits obtaining fully bacterial free protein particles, keeping the conformational status of the embedded proteins and the mechanical properties of the full aggregates.