Purpose: The purpose of this paper is to deal with an optimal consolidation problem for fresh agricultural products (e.g. fruits and vegetables) in a multi-temperature joint distribution (MTJD) system that is developed to resolve the challenge of timely delivery of small and diverse shipments in food cold chains. Design/methodology/approach: An integer programming optimization model is developed to consolidate a set of agricultural shipments with different storage requirements into a number of distinct containers according to the classification criteria. The formulated model for consolidating fresh agricultural products is evaluated using numerical examples. Findings: Critical factors that affect the quality or shelf life of fresh agricultural products are examined to form the criteria for classifying the storage requirements of these products. The formulated model can minimize the consolidation cost and the loss of product value due to a reduction in shelf life after consolidation. Research limitations/implications: Although the decision model for product consolidation developed in this paper takes into account practical concerns as much as possible, some additional conditions in the cold chain of fresh fruits and vegetables can be included to further enhance the application of the proposed consolidation model. Practical implications: Provided that the container environment is appropriately controlled, the shelf life of fresh fruits and vegetables can be maintained during the logistics process. As a result, product quality can be managed to reduce product loss. Originality/value: This paper adopts temperature, relative humidity and ethylene production, which generally affect the quality and shelf life of fresh agricultural products, as the main factors for determining the product consolidation. It is among the first to deal with the optimal consolidation of fresh agricultural products in the MTJD system with the consideration of product shelf life.