Production of enzymes through solid-state fermentation (SSF) of agro-industrial wastes reports high productivity with low investment. The extraction of the final product from the solid waste and solid disposal represent the main cost of the process. In this work, the complete downstream processes of SSF of two industrial residues for the production of proteases, soy fibre (SF) and a mixture of hair and sludge (HS), were studied in terms of activity recovery, using different extraction parameters (extracting solvent, ratio solid: solvent and extraction mode). Activity after lyophilisation was tested. Solid waste valorisation after extraction was studied using respiration techniques and biogas production tests, as part of a zero waste strategy. Results showed a maximum extraction yield of 91% for SF and 121% for HS, both in agitated mode and distilled water as extraction agent. An average activity recovery of 95 ± 6 and 94 ± 6% for SF and HS, respectively, was obtained after lyophilisation and redissolution. To reduce the cost of extraction, a ratio 1:3 : solid-solvent in static mode is advised for SF, and 1:2 : extraction ratio in agitated mode for HS, both with distilled water as extracting agent. Both composting and anaerobic digestion are suitable techniques for valorisation of the waste material.