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<i>Xanthomonas citri</i> subsp. <i>citri</i> (<i>X. citri</i>) is an important phytopathogen and causes Asiatic Citrus Canker (ACC). To control ACC, copper sprays are commonly used. As copper is an environmentally damaging heavy metal, new antimicrobials are needed to combat citrus canker. Here, we explored the antimicrobial activity of chalcones, specifically the methoxychalcone BC1 and the hydroxychalcone T9A, against <i>X. citri</i> and the model organism <i>Bacillus subtilis</i>. BC1 and T9A prevented growth of <i>X. citri</i> and <i>B. subtilis</i> in concentrations varying from 20 µg/mL to 40 µg/mL. BC1 and T9A decreased incorporation of radiolabeled precursors of DNA, RNA, protein, and peptidoglycan in <i>X. citri</i> and <i>B. subtilis</i>. Both compounds mildly affected respiratory activity in <i>X. citri</i>, but T9A strongly decreased respiratory activity in <i>B. subtilis</i>. In line with that finding, intracellular ATP decreased strongly in <i>B. subtilis</i> upon T9A treatment, whereas BC1 increased intracellular ATP. In <i>X. citri</i>, both compounds resulted in a decrease in intracellular ATP. Cell division seems not to be affected in <i>X. citri</i>, and, although in <i>B. subtilis</i> the formation of FtsZ-rings is affected, a FtsZ GTPase activity assay suggests that this is an indirect effect. The chalcones studied here represent a sustainable alternative to copper for the control of ACC, and further studies are ongoing to elucidate their precise modes of action.