In this work the dynamic study of EPS (Extracellular Polymeric Substances) concentration and distribution during the operation of two different reactor configurations (UASB and EGSB) is presented, treating medium (5 g COD/l) and low-concentrated (0.5 g COD/l) wastewater. Medium-concentrated wastewater was supplied for granules maturation as well as for stabilisation of the process. The effect of substrate change on granule characteristics was followed in both reactors. Total concentration of EPS associated to steady operation, was higher in the UASB reactor. The change to a low-concentrated substrate led to an increased difference, promoting a sharp destabilisation of the EGSB reactor, observing an increment in filamentous structures, causing biomass flotation and wash out. Although total concentration of EPS remained almost constant in the UASB reactor, their composition and distribution presented significant differences. The ratio of protein/polysaccharides as well as acidic-polysaccharides/total (neutral + acidic) polysaccharides decreased drastically in the EGSB reactor, while in the UASB reactor, the decrease was not so important and not enough for destabilisation of granule structure. Moreover, polysaccharides distribution seemed to have an important role in granule stability being enough to maintain granule cohesion only in the case of the UASB reactor. These observations point to composition and distribution of EPS rather than their total concentration as key parameters for granule stability and settleability.