Household waste represents a major source of energy, nutrients, and recyclable material. In order to exploit benefits and avoid hazards in the context of circular economy, the risk profile towards human and the environment should be assessed. Here, we investigated the presence of micropollutants by quantitative target analysis, suspect and non-target screening and evaluated changes in the chemical fingerprint upon anaerobic digestion. Extracts were analyzed by reversed phase liquid chromatography high-resolution mass spectrometry (LC-HRMS) and gas chromatography mass spectrometry (GC-MS). Thirty-one of 51 target micropollutants were detected in low ng/mL levels except for few detections at µg/mL levels. The micropollutants quantified in this study included the following: pharmaceuticals (salicylic acid, amitriptyline, carbamazepine); biocides (triclocarban, 2-phenylphenol); industrial compounds used in, e.g., paper industry (pentachlorphenol, PFOS, PFOA, bisphenol A); aromatics, polycyclic aromatics, and heteroaromatics, and their alkylated, hydroxylated, or carboxylated analogues. Fifty of 206 compounds from the suspect screening list were tentatively identified. These included phthalates, methylparaben, phenol, benzophenone, and pharmaceuticals, e.g., ibuprofen. Most compounds detected by GC-MS decreased more than twofold in peak height or remained unaffected by the anaerobic digestion, and very few increased more than twofold, e.g., p-cresol, menthol, and octadecanal. From the LC-HRMS non-target screening analysis, 250 chemical components were resolved using the multiway curve resolution technique PARAFAC2; of these, carbidopa was the only identified unknown.