This study highlighted the inorganic fractions in the extracellular polymeric substance (EPS) extract from two activated sludges and one biofilm. Nine EPS extraction methods (centrifugation, sonication, cation exchange resin (CER) + sonication, CER, heating, formaldehyde + heating, formaldehyde + NaOH, ethanol and EDTA) were used in the study. The EPS extracts had large inorganic fractions, which ranged from 28% to 94% of the EPS dry weight. The EPS inorganic fraction was dependent on the source of the sludge and wastewater, the kinds of bacteria and the extraction method. The EPS extracts obtained by heating and sonication had smaller inorganic fractions than those obtained by centrifugation. The compositions of the inorganic fraction of EPS extracts obtained with CER and sonication + CER showed similar trends. The chemical extraction methods could contaminate the inorganic composition of EPS extracts by impurities, carrying over of the extractant itself or by changing the pH of the solution. Ethanol was the most effective extractant for obtaining inorganic ions.