The study of the temperature gradients in cold stores and containers is a critical issue in the food industry for the quality assurance of products during transport and for minimising losses. This work presents an analysis of the temperatures during the refrigerated transport of 4,320 kg of blueberries in a reefer (set point temperature at −1°C) on a container ship from Montevideo (Uruguay) to Verona (Italy). The monitoring was performed by using semi-passive RFID loggers (TurboTag cards). The objective was to carry out a multi-distributed supervision using low-cost, wireless and autonomous sensors for the characterisation of the distribution and spatial gradients of temperatures during a long distance transport. Data analysis shows spatial (phase space) and temporal sequencing diagrams and reveals a significant heterogeneity of temperature at different locations in the container, which highlights the ineffectiveness of a temperature control system based on a single sensor, as is usually done.