Agroindustrial waste is considered to be a valuable secondary raw material for various industrial processes and the separation of various functional constituents due to its high availability and an interesting chemical composition, while simultaneously reducing environmental burden and costs. The aim of this paper was to investigate the use of a chelating agent (EDTA) and the influence of extraction parameters on the yield and composition of pectin from onion biomass waste. For the purpose of characterisation of pectin isolates and of residues after extraction, a characteristic method of high performance liquid chromatography (HPLC) was developed. The HPLC method determines 7 neutral sugars and 2 uronic acids, whereby the structural carbohydrates occupy most of the carbohydrate fraction. The highest yield of pectin substances was obtained in the sample extracted at elevated temperature and elevated pH of solvent. All pectin isolates had a dominant share of galacturonic acid, hence the most common type of pectin is homogalacturonan, whereas in the residues after extraction dominated glucose. This paper also presents balances for characteristic pectin monosaccharides (galacturonic acid, rhamnose, galactose and arabinose). Total utilization of galacturonic acid is favoured by elevated temperature and lower pH, whereas rhamnose, galactose and arabinose favor lower temperature and lower pH. Considering total utilization, the relative utilization of certain monosaccharides within the pectin fraction and residues fraction is also shown.