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To investigate the effect of harvest height on the amassed elements and ash content of Hyssop (Hyssopus officinalis L.), an experiment was conducted in a randomized complete block design with three replications. Treatments included four harvest heights, i.e., 15, 25, 35, and 45 cm (from the tip of the plant) and the residual stalks. The dependent variables were the amassed content of elements N, K, P, Ca, Mg, Cu, Zn, and Pb in different heights of the plant and the associated ash content (total ash (TA), acid-insoluble ash (AA), and water-insoluble ash (WA)). The results showed that by moving from the upper shoots toward the ground, the amassed content of Mg, Ca, Cu, Zn, and Pb increased by 22.67%, 43.74%, 12.87%, 39.02%, and 85.04%, respectively. Further, a downward trend was observed for N (50.16%) and K (6.41%) content, while an upward trend reported for P (29.06%) content. As for the residual stalks, by moving from the upper shoots toward the ground, Mg, Ca, Cu, Zn, and Pb contents decreased by 1.01%, 21.03%, 9.11%, 17.02%, and 51.06%, respectively, while N and P contents increased by 60.59% and 3.15%, respectively, and a 34.74% increase was seen in P content. With increasing harvest height, TA, AA, and WA values increased by 33.48%, 27.03%, and 18.25%, respectively. As for the residues, these variables increased by 11.44%, 6.35%, and 5.22%, respectively. Our results showed that 15 cm harvest height had the highest quality with the lowest heavy metal content. Graphical Abstract.