Lignin and manganese peroxidase (LiP, MnP) and laccase production by Phanerocheate chrysosporium was optimized by response surface methodology for brewery waste and apple pomace. The effect of moisture, copper sulphate, and veratryl alcohol (VA) concentrations on enzyme production was studied. Moisture and VA had significant positive effect on MnP and LiP production and the viability of P. chrysosporium (p < 0.05) and copper sulphate produced a negative effect. However, moisture and copper sulphate had a significant positive (p < 0.05) effect on laccase production, but VA had an insignificant positive effect (p < 0.05). Higher values of MnP, LiP and viability of P. chrysosporium on apple pomace (1287.5 U MnP/gds (units/gram dry substrate), 305 U LiP/gds, and 10.38 Log 10 viability) and brewery waste (792 U MnP/gds and 9.83 Log 10 viability) were obtained with 80% moisture, 3 mmol/kg VA, and 0.5 mmol/kg copper. LiP production in brewery waste (7.87 U/gds) was maximal at 70% moisture, 2 mmol/kg VA, and 1 mmol/kg copper. Higher production of laccase in apple pomace (789 U/gds) and brewery waste (841 U/gds) were obtained with 80% moisture, 3 mmol/kg VA, and 1.5 mmol/kg copper. Thus, moisture along with VA and copper sulphate was pertinent for the production of ligninolytic enzymes and increased cell viability.