Apple juice and apple cider were inoculated with Escherichia coli K-12 and processed using a high-pressure homogenizer to study bacterial inactivation. Seven levels of pressure ranging from 50 to 350 MPa were used in the high-pressure homogenizer. Two types of chitosan (regular and water soluble) with 2 levels of concentration 0.01% and 0.1% were investigated for synergistic effect with high-pressure homogenization for the bacterial inactivation. E. coli K-12 inactivation was evaluated as a function of homogenizing pressure at different concentration of 2 types of chitosan in apple juice and cider. High-pressure homogenization (HPH) induced significant inactivation in the range of 100 to 200 MPa, while thermal inactivation was the primary factor for the bacterial inactivation above 250 MPa. Significant (P < 0.05) 2-way interactions involving pressure and type of substrate or pressure and chitosan concentration were observed during the study. The homogenization pressure and the incremental quantity of chitosan (both types) acted synergistically with the pressure to give higher inactivation. Significantly (P < 0.05) higher inactivation was observed in apple juice than apple cider at same homogenizing pressure. No effect of type of chitosan was observed on the bacterial inactivation.