The effects of solvents and heating temperatures on the recovery and degradation of gel-forming EPS (Extracellular Polymeric Substances) extracted from aerobic granular sludge were investigated. Sodium hydroxide has allowed a better EPS solubilization compared to sodium carbonate (711.3 ± 38 and 408.4 ± 4 mg VS /g VS respectively) but the capacity to precipitate gel-forming EPS at acidic pH was higher in sodium carbonate (22% compared to 6% in sodium hydroxide at 80 °C). Increasing the temperature from 20 °C to 80 °C during EPS solubilization has multiplied the amount of solubilized matter by 4 in sodium carbonate and 2.2 in sodium hydroxide. Similar biochemical composition but different molecular weight profiles were observed for the two solubilized EPS extracts, evidencing partial degradation of the polymers in sodium hydroxide. Furthermore, coupling molecular weight analysis and precipitation yield measurement revealed that the lower precipitation of sodium hydroxide solubilized EPS is related to the size reduction due to degradation. Altogether these results help to guide towards a unified protocol for the extraction of gel-forming EPS.