In the current study, the Zygomycetes fungus Cunninghamella elegans NRRL Y-1392 was evaluated for its ability to grow in extracts derived from dried and ground agricultural residues, such as mushroom stalks and roots from hydroponically cultivated lettuces and produce poly-unsaturated fatty acids (PUFA) and γ-linolenic acid (GLA) rich lipids. Initially, the compositions of stalks and lettuce roots were analysed, and the fungus was batch-flask cultivated on six different commercial semi-defined substrates containing different sugars detected in stalks and roots to evaluate its catabolic ability. C. elegans was capable to assimilate all sugars, but at a lower rate in the case of arabinose. Subsequently, C. elegans was cultivated on tailor-made semi-defined commercial substrates, resembling hydrolysates containing carbohydrates found in mushroom stalks, under both nitrogen-excess and nitrogen-limited conditions, and resembling that of hydrolysates of roots, under nitrogen-excess conditions. Based on the results, under nitrogen-excess conditions, in the case of media resembling stalks hydrolysates, higher production values for biomass, PUFAs, and GLA were observed (20.3 g/L, 1906 mg/L, 668 mg/L), accompanied by high productivity values due to short cultivation periods, while under nitrogen limitation, high lipid accumulation (lipid in dry cell weight =48%, w/w) was presented, and lipids rich in oleic acid were produced. Finally, the fungus was cultivated on a medium derived from hot water-extraction applied to mushroom stalks, enriched with organic nitrogen sources. The fungus was successfully grown on the sugar-rich water-extract derived from mushroom stalks, resulting in dry biomass of 14.5 g/L, lipids of 1.8 g/L, with 15% (w/w) of GLA in cellular lipids.