It is still contentious how the abundance and diversity of magnetofossils reflect varying paleoenvironmental conditions. Here, we apply rock magnetic methods and transmission electron microscopy to identify magnetofossils in the core MD01‐2444 from the southwestern Iberian margin during the period 49.6–18.5 ka and 193.8–171.7 ka. Results show a correlation between the biogenic magnetite component and contrasting paleoenvironmental conditions. Specifically, remanence ratio (M_rs/M_s), the ratio of anhysteretic susceptibility (χ_ARM) to saturation isothermal remanant magnetization (SIRM), fractions of biogenic soft and biogenic hard components (BS + BH), and delta–delta ratio (δ_FC/δ_ZFC) have a negative relationship with planktonic δ¹⁸O, suggesting that more magnetofossils existed in sediments during warmer periods. Combining transmission electron microscopy images with paleoenvironmental proxies, we found that the proportions of bullet‐shaped magnetofossils increased in a warmer and less oxic environment, while isotropic shapes dominated in cooler and oxic environments.