Background: Rare earth elements (REEs) are present in agricultural ecosystems, but their baseline soil–plant transfer dynamics require systematic understanding. This study investigated the ‘source-to-sink’ biogeochemical distribution of REEs in soybean under background soil conditions. Methods: We characterized REE concentrations and fractionation patterns in the composite surface soil samples and analyzed two soybean cultivars (‘Jiyu 201’ (JY) and ‘Ping’an 16’ (PA)). A seven-stage sampling scheme (20–80 days post-sowing) using whole-plant samples was employed to evaluate temporal concentration dynamics, followed by discrete organ-level analysis at maturity. Results: The composite surface soil samples exhibited a light REE (LREE)-enriched signature with negative cerium (Ce) and europium (Eu) anomalies. While plants consistently mirrored the soil’s negative Eu anomaly, an observable shift toward a positive Ce anomaly was detected in plant tissues during the 45–65 days post-sowing window. REE concentrations were markedly higher in roots than in aerial tissues, indicating strong root-associated retention and limited acropetal translocation; however, the root values include both internalized and surface-associated fractions. Acropetal transport was accompanied by preferential LREE enrichment. Final organ-level partitioning was highly genotype-dependent: the indeterminate cultivar PA accumulated higher REEs in beans, whereas the sub-determinate cultivar JY retained them primarily in vegetative stems. Conclusions: Under background soil conditions, REE uptake and partitioning in soybean exhibit dynamic and genotype-dependent patterns. The observed shift in the Ce anomaly presents a notable biogeochemical phenomenon. Establishing these baseline dynamics is vital for evaluating crop elemental homeostasis and utilizing REEs as biogeochemical tracers.