Amendment of soil with organic urban and animal wastes can keep arable soil fertile without the need for synthetic fertilizers. However, pollutants present in these types of waste might be carried into the soil with unintended consequences for the environment. We studied an experimental agricultural plot, which had been amended with either synthetic inorganic fertilizers, human urine, manure, or wastewater treatment sludge at very high rates. We applied chemical non-target analysis to characterize present organic micropollutants, intending to compare treatments and highlight suspects of environmental concern. Soil samples were prepared by pressurized liquid and purified with solid-phase extraction before analysis with nanoflow ultra-high performance liquid chromatography coupled to high-resolution Orbitrap tandem mass spectrometry. Automated elucidation with two mass spectral libraries, multiple large chemical databases and environmental NORMAN suspect lists was able to annotate (level 3 and level 2) ∼ 20% of the 2306 detected features. A following principal component- and differential-analysis could separate the soil treatment groups’ pollution profiles and highlight high relative abundance features. From cattle manure, natural compounds such as bile acids and steroids were found. Human urine led to pollution with common pharmaceuticals such as metoprolol and propranolol. The highest number was added by wastewater treatment sludge, with 25 significant contaminants, spanning blood pressure regulators, antidepressants, synthetic steroids and sleep medication. Furthermore, using Kendrick mass defect plots, a series of polypropylene glycols could be revealed in the soil. Non-target analysis appears to be a promising method to characterize organic pollutants in soils.