Food fraud remains an issue with significant environmental, health, and socio-economic impacts for consumers and the food industry alike. Honey, known for its natural sweetness, rich nutritional value, and numerous health benefits, is among the most adulterated foods found in the global market. Common fraudulent practices include mislabelling the honey’s botanical origin, blending it with lower-quality honeys, processed sugars, or other substances. Moreover, as most of their beneficial properties are linked to honey’s botanical origin, it is important to assure the safety and quality of the honey. Nonetheless, with the increasing number of reports on tampered or adulterated products appearing, there is a pressing need to develop an analytical tool that can quickly, affordably, and reliably ensure the quality and safety of honeys. In this study, an innovative inkjet-printed gold electrode paper-based biosensing platform coupled with gold-coated magnetic nanoparticles (MNPs) was developed to detect the genomic DNA of two plant species from which honey can be produced: Castanea sativa and Erica arborea. Analyzing public database platforms, a DNA-target probe for both C. sativa and E. arborea were selected and designed. These sensors resulted from the DNA hybridization reaction between the two complementary probes specific to both plant species in a sandwich format. Their complementary probes were modified with an amine (NH₂) group and a fluorescein isothiocyanate and cut in two to generate the enzymatic amplification of the electrochemical signal. The hybridization reaction was labeled with enzymes, enabling chronoamperometric measurement of peroxidase activity associated with the MNPs on the gold electrode surface. The developed biosensor was then successfully applied to detect C. sativa and E. arborea present in real plant samples and, hence, determine the botanic origin of the honeys. Therefore, these MNPs and paper-based biosensors are a viable and rapid tool to help authenticate the origin of honeys.