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We developed and characterized a paper-based microfluidic sensor for the on-site diagnosis of drought stress in plants. Proline was used as a biomarker for analyzing drought stress, which was extracted by a colorimetric method using the proline-ninhydrin reaction. Paper was used as the main sensor material for the on-site detection of proline as it is easily transportable and cost-effective. The paper-based sensor was fabricated using wax-printing and origami methods, and the sensor was precoated with ninhydrin to allow for easy and convenient on-site use. Furthermore, a sample-to-ninhydrin ratio of 1:2 was found to confer optimal sensitivity to the drought diagnosis sensor. The concentration of proline in a sample was quantified by red-green-blue analysis to determine the change in green color intensity levels in response to distinct proline concentrations, which were detected by the sensor. The limit of detection of proline using the devised sensor was 657 µM, and the green color intensity level decreased with increasing proline concentration. In addition, the sensor was validated in an experimental drought stress model with Arabidopsis and subjected to drought stress for 21 days, and the amount of proline detected was 10 mM. The devised paper-based microfluidic sensor highlights the possibility of the on-site evaluation of drought stress in plants with potential to be utilized in various agricultural areas in the future.