Apple pomace constitutes a major waste stream of the food processing industry that is characterized by high concentrations of free sugars and structural carbohydrates. This study comparatively explored alternative apple pomace valorization strategies. To this regard, the integration of hydrothermal and organic acid pretreatment as a strategy to enhance anaerobic digestion biomethane yield and alternative production of mycoprotein as a valuable secondary product via the use of Aspergillus oryzae and Neurospora intermedia edible fungi were investigated. In scenario 1, both pretreatment liquors and solid residues underwent anaerobic digestion to produce biomethane. In scenario 2, pretreatment liquors and solid residues underwent fungal cultivation and anaerobic digestion, respectively. Additionally, to optimize bioenergy yield and minimize wastewater generation in scenario 2, the fungal growth effluent was also subjected to anaerobic digestion. In scenario 1, employing methane for transportation showed the potential to decrease GHG by 314.8 kt CO2 eq, translating to US$72.4 million in social cost savings. Similarly, in scenario 2, replacing edible fungal biomass in the food market could lead to a substantial reduction in emissions by 824.2 kt CO2 eq and a corresponding US$227.0 million in social cost savings.