Human and animal source-separated urine, stored and allowed to naturally hydrolyse (the bio-catalysed transformation of urea to ammonia and bicarbonate), has been used for millennia as a fertiliser in agriculture. In a context of growing water scarcity and climate uncertainty, source-separation of urine is facing a strong revival thanks to the emergence of cost-effective waterless collection systems. Concomitantly, urine source-separation can be used as a method for nutrient recovery and subsequent reuse. In its simplest form, such recovery consists of collection followed by urea hydrolysis and storage as sole treatment. Numerous guidelines, including by the World Health Organisation, consider that this is sufficient to stabilise the nutrients and inactivate any potential pathogens in the urine. However, it is still unclear whether said urine is effectively free from other compounds of concern, such as anthropogenic micropollutants with known toxicological effects. Moreover, it is also currently unknown if the metabolites produced by human consumption of these products behave in similar way during short- and long-term storage i.e. whether any changes in chemical structure mean that these could be sorbed and/or precipitated in a different way, or if they can potentially be degraded by the biomass inherently present in urine collection systems. Finally, there is currently no knowledge of whether the observed concentrations of micropollutants in stored hydrolysed urine could potentially have toxicological effects if/when applied to soils and edible crops. To fill these research gaps, 20 commonly consumed compounds were selected in this study and their concentrations in the liquid and solid phases studied in the short- and long-term (up to ≥ 2 years). During the initial process of urea hydrolysis (≤ 5 days), ethyl-glucuronide was the sole compound effectively removed (by deconjugation), while only two other compounds, erythromycin and its metabolite, saw a reduction in their concentration (likely due to biomass sorption). Subsequently, during early storage (≤ 15 days), only three additional compounds were removed: paracetamol (> 99%), acesulfame (11.5%) and carbamazepine-10,11 epoxide (40.7%). Finally, long-term storage of up to 24 months did not result in any further significant removal for any of the measured compounds, indicating that the procedure of hydrolysis + storage is not effective for the removal of anthropogenic micropollutants. The results of this investigation raise strong concerns about the direct reuse of hydrolysed/stored human source-separated urine, and evidence the need for post-processing before implementation as fertiliser into edible crops due to the inherent toxicological risk, particularly to infants.