Pretreatment technologies prior to anaerobic digestion (AD) have been developed with the aim of enhancing biogas productivity and reducing the presence of pathogens in digested sludge. Among them, thermal hydrolysis (TH) appears as the most promising one. In wastewater treatment plants (WWTPs) sludge is the end point of many organic micropollutants (OMPs), which was proved to lead to important environmental and human risks since sludge is commonly used in agriculture. The objective of this work is to determine the fate OMPs in TH and subsequent AD. Sewage sludge was pretreated in a TH pilot plant at 170 °C for 20 min. Afterwards, two anaerobic digesters with a working volume of 14 L fed with fresh and pretreated sludge were operated in parallel in mesophilic conditions. TH proved to be an effective technology to partially or totally remove the dissolved fraction of OMPs as well as the fraction sorbed into those suspended solids that are solubilised after this pretreatment. However, it did not affect the OMPs sorbed concentration into solids that are not solubilised. Globally, the OMPs removal efficiency during TH appears to be linked to the solids solubilisation during this process. Afterwards, the OMPs biotransformation efficiency in AD of fresh and pretreated sludge was determined. Noticeable differences between the microbiome of both reactors was determined, but the anaerobic biotransformation was not substantially different for most of the OMPs. However, it affected musk fragrances, which presented considerably lower biotransformation efficiency in the reactor fed with pretreated sludge. Therefore, TH was proved effective in partially removing OMPs but not in enhancing their bioavailability and subsequent anaerobic biotransformation.