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.