Water transported into Earth’s interior by subduction strongly influences dynamics such as volcanism and plate tectonics1,2,3. Several recent studies have reported hydrous minerals to be stable at pressure and temperature conditions representative of Earth’s deep interior, implying that surface water may be transported as far as the core–mantle boundary4,5,6,7,8. However, the hydrous mineral goethite, α-FeOOH, was recently reported9 to decompose under the conditions of the middle region of the lower mantle to form FeO2 and release H2, suggesting the upward migration of hydrogen and large fluctuations in the oxygen distribution within the Earth system. Here we report the stability of FeOOH phases at the pressure and temperature conditions of the deep lower mantle, based on first-principles calculations and in situ X-ray diffraction experiments. In contrast to previous work suggesting the dehydrogenation of FeOOH into FeO2 in the middle of the lower mantle9, we report the formation of a new FeOOH phase with the pyrite-type framework of FeO6 octahedra, which is much denser than the surrounding mantle and is stable at the conditions of the base of the mantle. Pyrite-type FeOOH may stabilize as a solid solution with other hydrous minerals in deeply subducted slabs, and could form in subducted banded iron formations. Deep-seated pyrite-type FeOOH eventually dissociates into Fe2O3 and releases H2O when subducted slabs are heated at the base of the mantle. This process may cause the incorporation of hydrogen into the outer core by the formation of iron hydride, FeHx, in the reducing environment of the core–mantle boundary.