Soil phosphorus (P) is usually hardly present in soluble forms as most of it is strongly bound to minerals. Therefore, transformations of soil colloidal P can play a key role in enhancing soil fertility. Here, we examined water extracts from a chronosequence of soils with 2000 years of paddy rice and 700 years of non-paddy cropping, and fractionated them into <1200 nm, <450 nm, and <3 kDa size fractions using sequential ultrafiltration. Asymmetric-flow field-flow fractionation (AF4) coupled to an organic carbon detector (OCD) and inductively coupled plasma mass spectrometry (ICP-MS) was used for organic carbon and elemental screening in the 3 kDa-450 nm colloidal size range. We found that P increased in all colloidal fractions both with long-term paddy rice and non-paddy managements. Furthermore, P in soil colloids of 3 kDa-450 nm size, as fractionated by AF4, peaked in three size ranges: nanoparticles (NP, ∼3 kDa-20 nm), fine colloids (FC, ∼20–225 nm), and medium-sized colloids (MC, ∼225–450 nm). The NP fraction originally contained mainly P and Ca for tidal wetland (TW), but turned into a complex of OC-Ca-P colloidal forms immediately after onset of arable management, with little temporal change thereafter. Fine colloidal P (FC-P) was detected only after > 50 years for the non-paddy and > 100 years under paddy management, associated with oxides, organic matter and fine clay fragments in the paddy soils and additionally Ca-bound P in the non-paddy ones, respectively. Increasing portions of medium-sized colloidal P appeared after 50 years paddy and non-paddy management, though not exceeding the concentrations of FC-P and with little changes during prolonged arable land use. Overall, after initial formation of FC-P during the first 50–100 years of management, longer term dynamics of colloidal P in these arable soils was fairly independent of paddy or non-paddy managements, but remained closely coupled to the increased presence or generation of fine colloidal clays, oxides and the associated P, thus potentially linking P fertility largely to the dynamics of fine colloids.