Trace organic contaminants (TOCs) correspond to a broad range of molecules generated either directly or indirectly by human activity. Even though TOCs are found at low concentrations in the environment, they often accumulate by biomagnification and bioaccumulation into biological organisms and cause irreversible damages in biological systems through direct or indirect toxic effects such as endocrine disruption and tumour initiation. This manuscript presents the main findings of over fifteen years of research focusing on biological removal of various TOCs found in sewage sludge from urban treatment plants. A special focus of the research was made on microbial processes in complex anaerobic ecosystems. Four families of compounds mostly retrieved in urban plants were studied: the polycyclic aromatic hydrocarbons (PAHs), the polychlorobiphenyls (PCBs), the phthalic acid esters (PAEs), and the nonylphenol ethoxylates (NPEs). It was observed that the microbial capability for removing low amounts of TOCs required a long adaptation time and was often limited by the bioavailability of these compounds. In fact, the overall biodegradation resulted from the numerous interactions existing between the matrix (organic matter) and the microbial ecosystems according to the physico-chemical sorption properties of these compounds. Mechanistic aspects were also tackled in depth and specific models were developed for better understanding the network of interactions between TOCs, microorganisms, and organic matter. These findings could be extrapolated to other ecosystems such as soils and sediments. Finally, it was shown that microbial cometabolism was essential for TOC removal, and the concept of bioavailability was not only dependent on the nature, the level, and the sorption properties of TOCs but was also strongly dependent on the nature and the concentration of the sludge organic matter. Specific parameters were proposed for better evaluating the fate of TOCs in microbial anaerobic processes and technological solutions for efficient removal of these compounds were also proposed.