An advanced oxidative process relying on the interaction of peroxymonosulphate and cobalt(II) was implemented for generating the sulphate radicals in flow analysis, in order to accomplish in-line sample preparation thus improving the spectrophotometric determination of phosphate and phosphite in liquid foliar fertilizers. To this end, a flow-batch system with a heated chamber was designed. The sample was handled twice, with and without the step of phosphite oxidation to phosphate, and the formed orthophosphate was quantified after interaction with the vanadate-molybdate reagent. Phosphite was determined as the difference in analytical signals corresponding to sample handling with and without the oxidation step. Influence of Co(II) on the peroxymonosulphate activation, reagent concentrations and added volumes, acidity, temperature and heating time were investigated like aiming at to improve analytical recovery and measurement repeatability, as well as the and system ruggedness. The 6.6–20.0 mg L−1 P2O5 standards were in-line prepared from a single stock solution. Detection limits were estimated as 0.8 and 0.1 mg L−1 for P2O5 and P-PO4. Twenty-four samples are were run per hour, and results are were in agreement with those obtained by the official procedure.