Organic contaminants are well recognized to be present in wastewaters and solid wastes such as sludge, manure, biowaste. Accurate analysis methods were developed to (i) better understand and model their fate during wastewater and solid waste treatments (industrial and lab-scale) thanks to their bioavailability assessment and (ii) reduce their impact in the receiving agroecosystems. Indeed, more than considering the total content of contaminants, organic bearing phases (aqueous extracts with various chemical accessibility) were well characterized all along the sludge treatment train, i.e. anaerobic digestion and compost. These processes impacted the bearing phases which drove the contaminants fate and distribution, which consequently impacted their fate after sludge application on soil.