Guaymas Basin is a young marginal rift basin in the Gulf of California, Mexico, characterized by active seafloor spreading and rapid sediment deposition, including organic-rich sediments. International Ocean Discovery Program (IODP) Expedition 385 drilled two sites near the Sonora margin, Sites U1549 and U1552, that are both close to a gas upflow pipe with Site U1549 being more distal to the corresponding upflow zone than Site U1552. Attenuated cold seepage conditions exist at Site U1549 in the central basin with methane occurrence below 25 meters below seafloor (mbsf), and hydrate was found to be present from ~25 mbsf at Site U1552. These two sites, ~12 km apart, represent an opportunity to study the influence of gas hydrate occurrence and methane seepage in shallow young organic-rich sediments (<170 mbsf; <0.29 Ma). In this data report, we present rock magnetic and geochemical data obtained from Sites U1549 and U1552 to characterize aqueous, solid iron, and sulfur phases present in the sediments, with a focus on iron oxides and iron sulfides. Guaymas Basin sediments are rich in reactive iron, mainly as pyrite. Iron oxides (magnetite and hematite) and authigenic iron sulfides (pyrite and greigite) are ubiquitously found in the sediments, and iron oxides are reduced to form pyrite. Pore water analysis seems to characterize current environmental and diagenetic processes, especially those related to fluid and gas circulation. Differences in methane seepage and hydrate occurrence could be due to spatial variations in methane fluid flow and pathways, leading to dynamic conditions at these sites with an impact on the sulfate reduction and anaerobic oxidation of methane rates. Authigenic magnetic mineralogy, mostly sensitive to biogeochemical processes at the sulfate–methane transition zone, would respond to fluid and gas flow variations, especially of methane.