The ultrafiltration membrane process is widely used for fruit juice clarification, yet the occurring of fouling promotes a decline in process efficiency. To reduce the fouling potential in the membrane application in food processing, the use of natural phenolic compounds extracted from cocoa pod husk is investigated. The cocoa pod husk extract (CPHE) was prepared in phenolic nanoparticles form and added into the polymer solution at varying concentrations of 0.5 wt%, 0.75 wt%, and 1.0 wt%, respectively. The composite membrane was made of a cellulose acetate polymer using DMF (dimethylformamide) and DMAc (dimethylacetamide) solvents. The highest permeability of 2.34 L m−2 h−1 bar−1 was achieved by 1.0 wt% CPHE/CA prepared with the DMAc solvent. CPHE was found to reduce the amount of Escherichia coli attached to the membranes by 90.5% and 70.8% for membranes prepared with DMF and DMAc, respectively. It is concluded that CPHE can be used to control biofouling in the membrane for food applications.