A multi-method protocol previously proposed for the extraction of extracellular polymeric substances (EPS) from flocculated sludges was investigated on dense aerobic granules. The protocol combines mechanical disruption by sonication and chemical extraction using the Tween detergent and the cation chelator, EDTA. Polysaccharides were mainly recovered during the first sonication step while proteins were recovered all along the extractive procedure with a high prevalence in the EDTA step. These data confirmed the interest of the multi-method protocol for harvesting a diversified pool of EPS from dense granules and for fractionation of the polymers according to their physicochemical properties. In addition, the high extractability of proteins with EDTA confers a specific behavior of the aerobic granules towards the multi-method extraction protocol, supporting the idea that proteins are associated in the granule matrix through ionic interactions involving divalent cations. Analysis of the extracted EPS by anionic exchange chromatography confirmed the presence of highly anionic proteins that were specifically detected in the extracts obtained from granules. One important question is now to investigate whether these highly anionic proteins are involved in the aggregation and densification process and if their presence is related to the cohesive properties of these particles.