Leaf scald (LS) caused by Xanthomonas albilineans (Xalb), is a major bacterial disease of sugarcane. The unreliable symptom expressions make traditional visual detection challenging. The molecular methods of detection require expensive equipment, labor-intensive, and time-consuming. This study proposes a novel electrochemical (EC)-approach, that is relatively easy to use and less expensive to detect Xalb DNA in LS-infected sugarcane leaves, meristematic tissue, and xylem sap samples. This method involves three key steps: i) DNA isolation from sugarcane samples via boiling lysis; ii) magnetic purification of target sequences from the lysate using magnetic bead-bound capture probes; and iii) EC detection of the target DNA. The method shows excellent detection sensitivity (10 cells µL−1), reproducibility (Standard deviation, SD <5%, for n = 3), and a wide linear dynamic range (1 nM–1 fM or 106–10° copies µL−1, r = 0.99). The EC assay has a strong negative correlation with quantitative polymerase chain reaction (qPCR) results (r = −0.95–0.97, n = 24, p < 0.001), and weak or no correlation with the varietal resistance ratings. This EC-based assay can be a commercially viable alternative, providing a DNA isolation/purification-free solution, and can potentially be adapted into a handheld device for on-farm detection and quantification of the LS-causing pathogen.