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Cultivation of cover crops is a valuable practice in sustainable agriculture. In cover crop management, the method of desiccation is an important consideration, and one widely used method for this is the application of glyphosate. With use of glyphosate likely to be banned soon in Europe, the purpose of this study was to evaluate the herbicidal effect of pelargonic acid (PA) as a bio-based substitute for glyphosate. This study presents the results of a two-year field experiment (2019 and 2021) conducted in northeast Germany. The experimental setup included an untreated control, three different dosages (16, 8, and 5 L/ha) of PA, and the active ingredients glyphosate and pyraflufen. A completely randomised block design was established. The effect of the herbicide treatments was assessed by a visual estimate of the percentage of crop vitality and a comparison assessment provided by an Ebee+ drone. Four vegetation indices (VIs) calculated from the drone images were used to verify the credibility of colour (RGB)-based and near-infrared (NIR)-based vegetation indices. The results of both types of assessment indicated that pelargonic acid was reasonably effective in controlling cover crops within a week of application. In both experimental years, the PA (16 L/ha) and PA_2T (double application of 8 L/ha) treatments demonstrated their highest herbicidal effect for up to seven days after application. PA (16 L/ha) vitality loss decreased over time, while PA_2T (double application of 8 L/ha) continued to exhibit an almost constant effect for longer due to the second application one week later. The PA dosage of 5 L/ha, pyraflufen, and a mixture of the two exhibited a smaller vitality loss than the other treatments. However, except for glyphosate, the herbicidal effect of all the other treatments decreased over time. At the end of the experiment, the glyphosate treatment (3 L/ha) demonstrated the lowest estimated vitality. The results of the drone assessments indicated that vegetation indices (VIs) can provide detailed information regarding crop vitality following herbicide application and that RGB-based indices, such as EXG, have the potential to be applied efficiently and cost-effectively utilising drone imagery. The results of this study demonstrate that pelargonic acid has considerable potential for use as an additional tool in integrated crop management. [ABSTRACT FROM AUTHOR]