The early diagnosis of plant pathogens from plant and soil samples needs a simple, rapid and cost-effective test, without the use of sophisticated and expensive equipment and reagents. In this study, the soil-borne pathogen Macrophomina phaseolina is used to demonstrate the potential for on-site molecular detection of the prototype diagnostic kit developed. This was achieved using a rapid and simple protocol comprising of a magnetic bead-based nucleic acid extraction, a portable PCR platform and a final NALFIA assay with a generic lateral flow device (LFD). The portable PCR platform powered by an external battery pack and all materials and reagents were included in a professional bag.