In the previous paper (Part I) in this series, a validated 3-D computational fluid dynamics (CFD) model of airflow and heat transfer inside a refrigerated shipping container (reefer) packed with apple was developed using porous media approach. In this paper (Part II), the cooling performance of commonly used package designs used for handling apple was investigated. First, the study computes the aerodynamic and thermodynamic characteristics of three package designs. This confirmed the effect of vertical airflow on the rate and uniformity of cooling inside the reefer. Then, the effects of vertical flow resistance on the rate and uniformity of cooling was further investigated. Adding vent-holes (3.5% vent area) on the bottom face of the package reduced vertical airflow resistance, and reduced the seven eighth cooling time by 37% compared to a package with no bottom vent-holes. The study demonstrated the significance of vent-holes on the bottom face of packaging boxes and the potential energy saving opportunities in refrigerated transport systems. (C) 2017 Elsevier Ltd. All rights reserved.