Relative abundances of goethite and hematite in marine sediments have been increasingly used in reflectance spectrometry studies to infer the precipitation regime at the source area of detrital sediments. This interpretation is contingent on the assumption that the ratio of these minerals is not modified by diagenetic processes. Our rock-magnetic study of the ~ 10.5–4.0 Ma interval of the Bengal Fan sedimentary sequence indicates that this is not always the case. We demonstrate that a statistical analysis of isothermal remanent magnetization acquisition curves provides an adequate estimate of the content of goethite and hematite in sediments. We also identified distinctive biogenic and “detrital” components (likely (titano-)magnetite or maghemite) in the studied samples. The sediments of the Bengal Fan contain a significant change in relative abundance of goethite and hematite at ~ 7 Ma, which is approximately coeval with a postulated climatic turnover in the sediment source region. However, systematic variations in the “detrital” and biogenic components, as well as an increase in the total organic carbon content and the appearance of pyrite concretions at the same stratigraphic level, suggest that this change in magnetic mineral content reflects a change in the degree of diagenetic alteration of the initial detrital assemblage rather than a climatic signal. When assigning climatic interpretations to changes in the relative abundance of goethite and hematite in marine sediments in future studies, the possibility of diagenetic modification should be evaluated. With rock-magnetic methods, alteration of ancient sediments can be detected and the severity of alteration can be estimated based on the presence and grain-size variation of the ferrimagnetic fraction (magnetite/maghemite), which is more sensitive to early reductive dissolution than high coercivity minerals (goethite and hematite).