The impact of molasses on the fungal mass, valuable secondary metabolites’ production and quality characteristics of the edible wild ascomycetous Morchella conica, strain AMRL78 was examined in this study. Morchella mycelium were produced in submerged, static and agitated cultures and the C/N ratio of the medium was determined to ~20. Evaluation included determination of the dry mycelial mass (X, g/L), endopolysaccharides synthesized (IPS, g/L), the consumption of total sugars (TS, g/L) and molasses’ phenolic-reduction and decolorization. The influence of agitation conditions was also evaluated. Results showed that M. conica appeared a significant production of dry mycelial mass (up to 16 g/L) and agitation had some impact upon X formation. A simultaneous high consumption of TS appeared both in agitated and static cultures. Maximum values of ~ 4.5 g/L IPS were recorded. M. conica reduced satisfactory phenolic compounds and the color of the molasse substrate (up to 46% and 20%, respectively). It is concluded that M. conica is a fungus of higher importance, amenable for simultaneous molasses detoxification and production of added-value compounds.