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 (Mrs/Ms), the ratio of anhysteretic susceptibility (χARM) to saturation isothermal remanant magnetization (SIRM), fractions of biogenic soft and biogenic hard components (BS + BH), and delta–delta ratio (δFC/δZFC) 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.