Edible wild ascomycetes Morchella rotunda, M. vulgaris and M. conica were cultivated in liquid static and agitated flasks of sucrose and molasses substrates with a C/N ratio of 20 and 25. The impact of four substrates on the production and quality characteristics of morels was examined. Evaluation included determination of the dry mycelial mass, intra-cellular (IPS) and extra-cellular (EPS) polysaccharides, total phenolic (TPC) and antioxidant (TAC) components, proteins, as well as the degree of phenolic content reduction and decolorization of molasses. The influence of agitation conditions was also evaluated. Results showed that substrate consumption, biomass formation and secondary metabolites production were substrate, species, and C/N ratio dependent. Among species, M. conica achieved the maximum biomass (18.16 g/L) and IPS (4.8 g/L) production and significant phenolic reduction (56.6%) and decolorization (26.7%). The maximum EPS (3.94 g/L) was noted by M. rotunda, whereas TPC (32.2 mg/g), TAC (6.0 mg/g) and cellular protein (7.6% w/w) were produced in sufficient amounts. These results strongly support the use of Morchella mushrooms as a biological detoxification agent of molasses in liquid fermentations and indicate their nutritional and medicinal value.