Applying organic wastes such as manure or sewage sludge on agricultural fields improves soil physical structure and fertility, while giving purpose to otherwise disposed and burned waste products. Yet, xenobiotics, and especially pharmaceuticals and personal care products, may be present in these wastes and thereby enter the soil ecosystem. To investigate their occurrence and their potential effect on soil fauna, the CRUCIAL experimental fields, Denmark, were used. Here we combine, for the first time, a chemical wide-scope suspect screening analysis with a study of soil nematode faunal response on soils, which were fertilized with cattle manure, sewage sludge, human urine, and mineral fertilizers over 14 years. The suspect screening analysis was performed with a nanoflow ultra-high performance liquid chromatography coupled with high-resolution tandem mass spectrometry. The abundance of soil indigenous nematodes was determined in each treatment at two time-points, followed by laboratory tests with the nematode species Caenorhabditis elegans to assess its reproduction capacity in the soils. A total of 12 pharmaceuticals and personal care products were identified as being up- or down-concentrated in the different treatments compared to controls (mineral fertilizers): 8 and 2 were found to be up-concentrated in sludge- and urine-treated soils, respectively. Our results, however, showed a significantly greater abundance of nematodes in soils amended with sludge and manure, while C. elegans had the lowest reproduction capacity in the controls. The reproduction capacity tests did not reveal any chronic toxicity. A principal component analysis showed a clear correlation between nematode abundance and soil organic matter, water content, nutrient contents, and porosity. Overall, urban and animal wastes enhanced soil quality. Pharmaceuticals were detected, but adverse effects on the measured endpoints could not be demonstrated. Although further investigations are needed to examine other associated risks, recycling nutrients from urban areas into fertilizers can contribute to a more sustainable fertilization strategy.