The organic matter content in original and chemically treated olive mill wastewater was profiled by structural fractionation to evaluate changes in its characteristics after acid cracking and electrocoagulation processes. For this purpose, the effluent was subjected to a resin fractionation method and results were evaluated in terms of the parameters COD, TOC, total phenols, color (as absorbance), acute toxicity using Vibrio fischeri photobacteria and Fourier Transform Infrared (FTIR) spectroscopy. Significant amounts of oil-grease (95%) and particulate matter (96%) corresponding to 58% COD, 43% TOC, 39% total phenols and 80% color removals were obtained by acid cracking. After subsequent electrocoagulation with stainless steel electrodes, total phenols removal rates increased from 39% to 72%, while no significant additional COD and TOC removals (10-15%) were evident. Fractionation results demonstrated that the organic matter present in the original effluent was mainly of hydrophobic nature (75-95%). For the total phenols parameter, a significant fraction (56%) appeared to be hydrophobic neutral that matched the 75% toxic (inhibitory) effect of the wastewater. After chemical treatment, a shift was observed from mainly hydrophobic to hydrophilic fractions for the COD and TOC parameters, and the inhibitory effect of treated effluent increased from 75% to 89%. FTIR results indicated a loss of aliphatic structures together with an increase in aromatic structures after chemical treatment that was related to the increase in the inhibitory effect of the treated effluent.