Homogeneity and temperature levels within a refrigerated facility are vital in preserving the quality of horticultural products throughout the cold chain to the consumer. These temperatures are affected by different factors at different scales, including the shape and thermal properties of the horticultural products, package design, pallet arrangement, or characteristics of the cold chain unit of operation. Therefore, airflow and heat transfer studies are valuable in evaluating these factors to optimize the cold chain and achieve and maintain an optimal product temperature. This paper provides an overview of the different scales of the numerical model and experimental setup used to assess the influence of the different factors on the cooling performance, as well as any challenges and limitations of each scale. The importance of considering other aspects in the cold chain studies, such as product quality, energy consumption, and package mechanical strength, will be discussed through an integrative approach. Finally, we propose new perspectives on how multi-scale modelling approaches can be helpful in tackling different challenges and how to investigate the effects of different factors on the cooling efficiency.