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• NPF5.9 acts independently of its NPF5.8 homolog to detoxify heavy metals. • NPF5.9-mediated As and Cd detoxification occurs specifically under Fe-deficient conditions. • Detoxification is independent of the known NPF5.9 substrates nicotianamine and nitrate. • NPF5.9 detoxification activity depends on the thiol-based chelators GSH and PCs. Nutrient absorption in plants is often nonspecific, making them vulnerable to the uptake of hazardous chemicals or excessive amounts of essential elements. Toxic concentrations of heavy metals can disrupt cellular processes—ranging from DNA and protein stability to photosynthesis—and plants have evolved strategies to mitigate these effects. Phytochelatins—major plant metal detoxifiers—and their precursor glutathione are key thiol-based chelators that bind and sequester metals to reduce their toxicity. The Arabidopsis NPF5.8 and NPF5.9 transporters act redundantly in iron homeostasis; however, the distinct expression pattern of NPF5.9 under iron deficiency suggests it may play a specific role under these conditions. Given the interplay between iron nutrition and metal homeostasis, we used reverse genetics and epistatic analyses, complemented with heterologous expression in yeast, to explore NPF5.9’s role in the response to heavy metals. We found that NPF5.9 detoxifies arsenic and cadmium specifically under conditions of iron starvation. This function is not mediated by its reported substrates, nicotianamine and nitrate, but instead depends on glutathione and phytochelatins. Unlike its role in iron transport, NPF5.9-mediated detoxification operates independently of NPF5.8, although both functions rely on substrate redistribution through vesicular transport. Overall, our results indicate that iron deficiency triggers NPF5.9 gene expression and likely shifts its substrate preference toward thiol-based chelators. These chelators are distributed intra- and intercellularly via early and late endosomes to mitigate arsenic and cadmium toxicity. NPF5.9 emerges as an example of the versatility of major facilitator superfamily transporters, potentially relying on different substrates to respond to various environmental cues.