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Summary Mitochondria and chloroplasts are organelles with high iron demand that are particularly susceptible to iron‐induced oxidative stress. Despite the necessity of strict iron regulation in these organelles, much remains unknown about mitochondrial and chloroplast iron transport in plants. Here, we propose that Arabidopsis ferroportin 3 (FPN3) is an iron exporter that is dual‐targeted to mitochondria and chloroplasts.FPN3is expressed in shoots, regardless of iron conditions, but its transcripts accumulate under iron deficiency in roots.fpn3mutants cannot grow as well as the wild type under iron‐deficient conditions and their shoot iron levels are lower compared with the wild type. Analyses of iron homeostasis gene expression infpn3mutants and inductively coupled plasma mass spectrometry (ICP‐MS) measurements show that iron levels in the mitochondria and chloroplasts are increased relative to the wild type, consistent with the proposed role of FPN3 as a mitochondrial/plastid iron exporter. In iron‐deficientfpn3mutants, abnormal mitochondrial ultrastructure was observed, whereas chloroplast ultrastructure was not affected, implying that FPN3 plays a critical role in the mitochondria. Overall, our study suggests that FPN3 is essential for optimal iron homeostasis.