Drawbacks of sample preparation can be overcome by mechanization, minimizing systematic errors and analysis time, as well as improving precision. Multi-pumping flow systems (MPFS) attain the requirements for mechanization in a versatile and robust way, minimizing reagent consumption and waste generation. A MPFS was proposed for the fractionation of water soluble phosphorus in cereals, which is important because the bioavailability of this nutrient depends on its chemical form. Besides, phytic acid yields stable complexes with some micronutrients (e.g. Fe3+, Ca2+ and Mg2+), thus also altering their bioavailability. The flow system incorporated on-line photochemical conversion of organic phosphorus to phosphate, which was quantified by the spectrophotometric molybdenum blue method. A linear response was observed between 5 and 40mgL−1 for both inorganic (PI) and organic (PO) phosphorus, with detection limits of 0.5 and 1.2mgL−1, respectively. Coefficients of variation (n=20) were estimated as 1.2 and 3.6% for PI and PO, respectively, with a sampling rate of 80 determinations per hour. Per determination, 380μg of (NH4)6Mo7O24, 620μg of ascorbic acid and 790μg of K2S2O8 were consumed, generating only 2.5mL of waste. Interferences of organic matter were avoided by sample pretreatment with active charcoal (20mg/mL). The results for cereal samples agreed with those obtained by the reference procedure based on nitro-percloric digestion. The proposed procedure is then a reliable, fast, inexpensive and more environmentally friendly alternative for phosphorus fractionation.