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Magnetofossils are nanosized magnetic fossil remnants of magnetotactic bacteria (MTB) that are widely distributed in marine and freshwater sediments. Past studies have revealed that changes in the morphology and abundance of magnetofossils are linked with diverse paleoenvironmental changes, such as glacial‐interglacial variation, redox conditions associated with primary productivity and organic matter supply, chemical weathering and diagenesis. Besides, it has long been speculated that changes in geomagnetic field intensity could also affect the abundance of magnetofossils. However, it is not yet clear, how these environmental factors controlled past MTB populations in combination. To answer this question, we studied magnetofossils‐rich sediments from cores MD01‐2443 and 2444 off the Southwest Iberian Margin. The paleomagnetic records of our samples reveal geomagnetic excursions corresponding to the Laschamp, Blake, Iceland Basin, and Pringle Falls events. We estimated the relative abundance of magnetofossils in the samples based on isothermal remanent magnetization unmixing and found it to increase during warmer periods and decrease during colder periods, while not covary with changes in the geomagnetic field intensity. To further distinguish the role of different paleoenvironmental factors, we compared magnetofossil abundance with planktonic δ18O, δ13C of organic matter, K/Al and Si/Al, which indicate continental ice volume (paleotemperature), organic matter origin, run‐off intensity and productivity, respectively. The results indicate that less continental ice volume (higher paleotemperature), enhanced productivity and run‐off intensity are closely related and jointly promoted magnetofossil production and preservation. Our study offers a comprehensive approach to understanding how magnetofossil assemblages relate to paleoenvironmental changes off the SW Iberian Margin. Plain Language Summary: Magnetofossils are inorganic remnants of a special kind of bacteria, called magnetotactic bacteria, which live in marine and freshwater sediments and produce tiny magnetic mineral particles for navigation. Previous studies found that magnetofossils can indicate the variation of the environment in the past. However, few studies focus on how magnetofossils vary with the variations in the Earth's magnetic field intensity. In this study, we selected samples of cores MD01‐2443 and 2444 off the Iberian margin to investigate how magnetofossils respond to the environmental change including the variation of geomagnetic field intensity from 18.5 to 49.56 ka and 104.78 to 223.92 ka. We distinguished four geomagnetic excursion events accompanied by a reduction in the geomagnetic field intensity. We applied a new hybrid unmixing method to determine the abundance of magnetofossils in our samples. Our results show that magnetofossil abundance has no relationship with the variation of geomagnetic field intensity. Besides, we used geochemical methods to determine the intensity of river‐off, productivity, and the origin of organic matter off the SW Iberian margin. Our results show that magnetofossils can be controlled by the multiple environmental factors mentioned above. Our study is helpful for better understanding the paleoenvironmental implications of magnetofossils. Key Points: We used a hybrid unmixing approach to quantify the relative abundances of magnetofossils in Quaternary marine sedimentsMagnetofossil abundance correlates with glacial‐interglacial change, productivity, and river run‐off off the SW Iberian marginAn impact of geomagnetic field intensity on magnetofossil content and composition is not apparent [ABSTRACT FROM AUTHOR]