Increasing attention is being given to magnetic iron-based nanoparticles (MINPs) because of their potential environmental benefits. Owing to the earth abundance and high utilization of MINPs, as well as the significant functions of Fe in sustainable agriculture and environmental remediation, an understanding of the environmental fate of MINPs is indispensable. However, there are still knowledge gaps regarding the largely unknown environmental behaviors and fate of MINPs in soil-plant system. Thus, this review summarizes recent literature on the biogeochemical behavior (uptake, transportation, and transformation) of MINPs in soil and plants. The different possible uptake (e.g., foliar and root adsorption) and translocation (e.g., xylem, phloem, symplastic/apoplastic pathway, and endocytosis) pathways are discussed. Furthermore, drivers of MINPs uptake and transportation (e.g., soil characteristics, fertilizer treatments, copresence of inorganic and organic anions, meteorological conditions, and cell wall pores) in both soil and plant environments are summarized. This review also details the physical, chemical, and biological transformations of MINPs in soil-plant system. More importantly, a metadata analysis from the existing literature was employed to investigate the distinction between MINPs and other engineering nanoparticles biogeochemical behavior. In the future, more attention should be given to understanding the behavior of MINPs in soil-plant system and improving the capabilities of predictive models. This review thus highlights the main knowledge gaps regarding MINPs behavior and fate to provide guidance for their safe application in agrochemicals, crop production, and soil health.