Purpose Polyphosphate (poly-P) fertilizers were proposed to increase the low phosphorus use efficiency (PUE) of orthophosphate (ortho-P) fertilizer but empirical data is inconsistent. Our study is aimed at investigating how soil properties, application time, and growth duration affect their phyto-availability.Methods Olsen-P dynamics were monitored using six soils amended with either ortho-P or poly-P. Subsequently, two contrasting soils (sandy and loamy) were selected to estimate P availability to plants using wheat as a model plant. Mechanistic modelling was used to interpret P dynamics in these experiments.Results For poly-P amended soils, Olsen-P increased continuously, while using ortho-P fertilizer the highest values were attained right after application and then monotonously decreased afterward. Olsen-P dynamics varied greatly among soils depending on their sorption capacity and related properties. In sandy soils, Olsen-P was consistently higher for ortho-P. In highly calcareous soils, Olsen-P was higher for poly-P after three weeks. Plant experiments confirmed a greater uptake of poly-P over ortho-P in loamy soil and extended trials (4 months) but not in sandy soils or short-term trials (4 weeks). Geochemical modeling suggested that complexation of soil Ca by poly-P reduced long-term P immobilization.Conclusions Soil properties and growth duration affect the efficiency of ortho-P vs. poly-P fertilizers. In clayey soils and extended growth duration, poly-P fertilizer can enhance PUE due to its prolonged phyto-availability as compared to ortho-P. In sandy soils and short growth duration poly-P has little advantage. The complexation of Ca by poly-P may have caused the increase of P phyto-availability.