The pre-treatment of both winery wastewater (WW) and olive mill wastewater (OMW) by coagulation, using a natural organic coagulant, was investigated as a possible alternative to conventional metal based coagulants, in order to produce a potentially reusable organic sludge. Chitosan was chosen as a model natural organic coagulant and the coagulation process was optimized investigating different coagulant doses and pH values. In spite of the notably lower polluting load for the WW compared to the OMW, the efficiency of the chitosan coagulation was found to be high in terms of total suspended solids (81% and 80% for OMW and WW respectively) and turbidity (94% and 92% for OMW and WW respectively) removal for both wastewaters, but a notable difference was observed in terms of organic matter removal (32% and 73% in terms of COD for OMW and WW respectively). Taking into account that the best performances of the coagulation process by chitosan were achieved at the actual pH for OMW as well as no significant differences were observed for WW as the pH was changed, no chemicals addition is required to adjust pH.