AbstractFerromanganese (FeMn) crusts are Fe and Mn oxides that typically form on deep‐sea elevations by deposition of colloids from seawater. These mineral deposits are considered a source of critical metals and rare earth elements. Besides their potential economic value, FeMn crusts are extremely relevant in ocean science, since their very slow growth rates result in long‐term paleoenvironmental and paleoceanographic records. In this study, we applied geochemical, mineralogical, and magnetic analyses to unravel paleoenvironmental changes at two locations on opposite sides of the Atlantic Ocean, the Rio Grande Rise in the SW Atlantic and the Tropic Seamount in the NE Atlantic. Our results show that the occurrence of amorphous (non‐crystalline) Fe oxyhydroxides and the absence of Fe oxides in hydrogenetic, non‐phosphatized FeMn crusts prevented the development of primary remanent magnetization. In contrast, phosphatized FeMn crusts may have contained a remanent magnetic signal. Phosphatization resulted from increased primary productivity and occurred at different stages during the growth of the FeMn crusts, leading to suboxic conditions and partial dissolution of pre‐existing, remanence‐carrying magnetic minerals. Carbonate Fluorapatite (CFA) accumulation in the phosphatized layers of FeMn crusts replaced Fe and Mn, decreasing their magnetic content. Thus, magnetic variations do not reflect a primary magnetization but rather result from geochemical alterations. The loss of primary magnetization may hamper the use of FeMn deposits for magnetostratigraphic purposes.