Urine has great potential to be an effective fertilizer due to its high nutrient content, however, it can contain potentially worrying pharmaceuticals. Our objective was to study whether urine storage and aerobic biological treatment, i.e. nitrification, was sufficient to remove pharmaceuticals or an additional treatment with activated carbon was necessary to produce a fertilizer from urine. We investigated the abatement of twelve pharmaceuticals, including antibiotics and antivirals, in laboratory experiments representing the treatment steps of anaerobic storage of source-separated human urine, stabilization using partial and full nitrification under acclimatized and non-acclimatized conditions, and treatment of nitrified urine using powdered activated carbon (PAC). Two-month-long-term storage of urine was insufficient to substantially degrade the pharmaceuticals, except for hydrochlorothiazide (>90%). In the partial and full nitrification fed-batch reactors, atazanavir, ritonavir, and clarithromycin were rapidly removed, with biotransformation rate constants greater than 10 L(gss)(-1)d(-1). Darunavir, emtricitabine, trimethoprim, N4-acetylsulfamethoxazole, sulfamethoxazole, atenolol, diclofenac, and hydrochlorothiazide were degraded slowly, with biotransformation rate constants of < 1 L(gss)(-1)d(-1). With 200 mg PAC L-1, at least 90% of each investigated pharmaceutical was removed. Yeast estrogen screen tests and bioluminescence inhibition tests revealed efficient removal of estrogenicity (99%) and toxicity (56%) using nitrification, and a reduction of 89% and 64%, respectively, using 200 mg PAC L-1. With our study, we provide biotransformation rate constants of compounds never previously investigated. We also show that a combination of nitrification and PAC adsorption enables the production of a safe fertilizer with sufficiently low pharmaceutical concentrations and no removal of beneficial nutrients.