Global agriculture trade stimulates a transformation of traditional cold chains to global cold chains with long-haul intercontinental transportation. Sea transportation by reefer containers will be the dominant modality in the future for global cold chains. Reefer logistics plan and control the forward and backward logistics of reefer containers and perishable products. One of the biggest challenges in reefer logistics is to find solutions balancing cost, quality, and sustainability since improving product quality and sustainability may come at a cost. Additionally, multiple stakeholders (e.g., shippers and transport operators) are involved in reefer logistics, who have different perceptions of the product quality, economic aspect, and sustainability. There can be a conflict of interests between stakeholders. Therefore, it is necessary to manage the potentially conflicting objectives in a multi-actor setting for reefer logistics. The main research question that this thesis aims to answer is: How to manage reefer logistics considering its distinctive characteristics and trading off conflicting objectives of multiple stakeholders? In this thesis, we firstly provide an overall understanding of reefer logistics by analysing its technical characteristics and stakeholders using the system analysis approach. After the qualitative analysis, we propose a generic agent-oriented modelling framework to manage reefer logistics, which considers the identified features and the multiple stakeholders’ objectives. We further evaluate two (re)designs of reefer logistics (viz. the application of remote monitoring technologies and a new concept of port-hinterland transport) using the overall understanding of reefer logistics and the generic modelling framework.