Three strains of Aspergillus oryzae were used for fungal protein production from starch processing wastewater (SPW) as part of a comprehensive SPW utilization and treatment program. The mycelial morphologies of the three strains varied from fluffy, clumpy mycelia to compact pellets with various strains and cultivation conditions of growth pH, inoculum quantity and superficial air velocity in an air lift bioreactor process. An inoculum technique was developed to ensure a desirable morphology with an improved fungal protein yield. Experimental relationship between the morphology and the yield revealed that the formation of small compact pellets under designed cultivation conditions favoured higher fungal protein yields, easier product separation and better process operation.