To meet the upcoming challenge of environmental sustainability, refrigerated transport is required to address energy efficiency and use sustainable fluids, namely natural refrigerants, at the same time taking into consideration the typical constraints of mobile systems, i.e. space and weight, system complexity, reliability and ease of servicing and maintenance. In this study, the design of a R744 refrigeration system employed on a light commercial vehicle used for urban delivery of fresh products (4-5 kW at 0°C) is considered. The effects of different system architectures, controls and components are numerically evaluated focusing on the trade-off between the increase of the unit complexity, leading to higher energy efficiency of the sole cooling system, and the decrease of the unit overall encumbrance and weight, leading to lower carbon footprint of the vehicle. Numerical results show that the use of an ejector can enhance the unit COP up to +28.6% for high ambient temperature conditions (40°C). A compact unit design based on the use of a light and efficient variable-speed scroll compressor leads to a reduction in carbon emissions of an average delivery mission between -17.9% and -34.4%, depending on climatic conditions. The effects of evaporator sizing on the system performance and emissions are discussed. The overall carbon footprint of the units over their entire life cycle is assessed, highlighting that more than 95% of the equivalent CO2 emissions are related to system operation. The use of natural refrigerant R744 reduces the direct leakage emissions to negligible values.