Mitochondria and chloroplasts are organelles with a high iron demand that are highly 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 show that Arabidopsis Ferroportin 3 (FPN3) is an iron exporter dual-targeted to mitochondria and chloroplasts. FPN3 is expressed in shoots regardless of iron conditions, but its expression in roots is regulated. fpn3 mutants cannot grow as well as wild type under iron-deficient conditions and shoot iron levels are reduced in fpn3 mutants than in wild type. Analysis of iron homeostasis gene expression in fpn3 mutants and ICP-MS analysis suggested that iron levels in the mitochondria and chloroplasts are increased, consistent with the proposed role of FPN3 as a mitochondrial/plastid iron exporter. In iron deficient fpn3 mutants, abnormal mitochondrial ultrastructure was observed, whereas chloroplast ultrastructure was not affected, implying that FPN3 plays a critical role in iron metabolism in mitochondria. Overall, we propose that FPN3 is crucial for iron homeostasis.