Continuous sequences of Cenozoic fluvial-lacustrine sediments are well preserved in the northeastern edge of the Tibetan Plateau (TP), and they provide a good opportunity to improve our understanding of the tectonic uplift and paleoenvironmental evolution of the NE TP. To date, however, the factors controlling the variations in the magnetic properties of these fluvial-lacustrine sediments remain complex and ambiguous. Here we systematically assess the contribution of pedogenesis to the magnetic enhancement of late Miocene fluvial-lacustrine sediments in the Xining Basin, using a combination of rock magnetic, diffuse reflectance spectroscopy, and geochemical methods. Our results demonstrate that the magnetic concentration parameters show a long-term increasing trend since the late Miocene, with two dramatic increases at similar to 11 and 9 Ma. Based on the examination of several factors that may affect the magnetic properties of fluvial-lacustrine sediments in the NE TP, we argue that an accelerated drying process in waterlogged environments, induced by late Miocene global cooling or/and tectonic uplift, may have caused the changes from anaerobic to aerobic conditions and resulted in the observed stepwise increases in pedogenic intensity. The two dramatic increases in magnetic parameters are closely related to intensified aridification and tectonic activity in the NE TP at similar to 11 and 9 Ma, respectively. These observations suggest that the pedogenic magnetic enhancement model, caused by the disappearance of a waterlogged and reducing pedogenic environment since the late Miocene, should be reconsidered as a possible factor explaining the magnetic properties of fluvial-lacustrine sediments in the NE TP.