Soil phosphorus management is critical in conventionally managed farms and organic farms. Knowledge about inorganic P (Pi) fractions, availability, and dynamics under different cropping systems; greenhouse and open field, locations with different climatic conditions (Al-Tuneib and Jordan Valley), and soil sampling dates (three dates) for medium- (5 years in Jordan Valley) and long-term (13 years in Al-Tuneib) organic farming is inadequate. Thus, this study was conducted to investigate the effect of these factors on soil Pi to assess the status of soil P to better manage organic farming, control stock soil P, and protect environment and water resources. Soil Pi sequential fractionation was performed using calcareous soil adapted procedure. Results indicated that Olsen P; a traditional P availability index, was higher in Al-Tuneib (in greenhouse) where possible P leaching can occur due to irrigation. Conversely, the most labile fraction (Ca2-P) was significantly higher in Jordan Valley (in greenhouse), particularly, at the beginning of the rotation cycle (D1). However, Ca2-P was higher in Al-Tuneib (in open field) at D1, whereas at D3 it was higher in Jordan Valley. Concerning the effect of cropping system, open field soils had generally higher Ca2-P, except at D1 in Jordan Valley. Regarding Pi dynamics, Ca2-P significantly increased over time, while the moderately labile fraction (Ca8-P) decreased, revealing an inverse correlation. Results indicated that Ca8-P was dynamically replenishing Ca2-P, providing insight into soil P dynamics in organic farming. Our findings will help managing soil P inputs, stock soil P and P leaching risk under organic farming.