Several thousand litres of liquid effluent waste are generated from the production of mycoprotein, at the Quorn Foods production facility in Billingham (UK) every day. All of this waste currently undergoes effluent treatment before disposal, despite the fact that potentially valuable mononucleotides are known to be present at significant concentrations in the waste. To harness these nucleotides, an extraction procedure was necessary. Polynucleotide extraction procedures are well reported, using methods such as precipitation, phenol-chloroform extraction or polyethylene glycol (PEG) extraction, but application of these methods for mononucleotide has not been reported, so significant adaptation of conventional protocols was necessary to ensure good recovery of mononucleotides, with specific consideration of the process operating industrially. Precipitation of nucleotides was identified as the most favourable option, after comparison of conventional laboratory-based extraction protocols. The effects of salt choice, salt molarity, solvent choice, solvent ratio, pH, incubation temperature, pre-treatment and product washing were all tested as a function of yield, purity, protein retention and salt contamination, using UV-Visible spectrophotometry, the bicinchoninic acid (BCA) assay and inductively-coupled plasma optical emission spectroscopy (ICP-OES). Results showed that 0.06 M magnesium acetate was effective at extracting mononucleotides at a yield of up to 50%, although higher yields may be possible following recommended further work. It is hoped that this method may be the basis for an industrial procedure for the large-scale extraction of nucleotides from waste, which can then be distributed to a number of active markets across the UK, Europe and beyond.