Protein aggregation is commonly observed in genetically engineered bacteria over-expressing foreign genes, in the context of protein production processes. Very often, recombinant polypeptides deposit as insoluble protein clusters named inclusion bodies, whose formation is driven by stereo-specific cross-molecular interactions between partially folded polypeptide chains. The formation of inclusion bodies has been historically considered as the main bottleneck in industrial production processes of proteins, since a wide diversity of protein species tend to aggregate in bacteria. As the formation of inclusion bodies can be eventually minimized but rarely prevented, aggregated polypeptides of industrial interest need to be refolded in vitro before use. However, the progressive understanding of the molecular and physiological mechanisms regulating aggregation has revealed that inclusion bodies contain significant amounts of biologically active protein species making them suitable for the straightforward use in different in vitro processes, as functional, particulate entities. Therefore, when formed by enzymes, inclusion bodies are catalytic particles ready for industrial use. As discussed here, the genetic background of the host bacteria and the protein production conditions can be adjusted to tune the biological and biophysical properties of bacterial inclusion bodies, to gain manipulability and to make them more biotechnologically friendly.