Non-uniform heating caused by uneven electromagnetic field distribution in a material is a major regulatory barrier for applying radio frequency (RF) heating in critical processes, such as pasteurisation of low moisture agricultural products. An earlier finite element model was adopted and validated to predict the temperature distribution in peanut kernels heated in a 6 kW, 27.12 MHz RF laboratory unit using 4.5 kg batches of peanut kernels. A temperature uniformity index (TUI) was used as a measure of the temperature distribution within the RF treated product load. The modelling results were used to demonstrate that the temperature distribution in RF heated peanuts could be improved by segregating samples into structured blocks with air gaps between them. The developed concept from this study can further be expanded to optimise industrial-scale RF treatment protocols for controlling microorganisms in agricultural products.