An autotrophic nitrogen removal bioreactor with granular biomass was exposed to high antibiotics concentration in order to evaluate its impact over the performance and the biomass of this bioprocess. A mixture of azithromycin, norfloxacin, trimethoprim and sulfamethoxazole caused loss of autotrophic nitrogen removal performance, coupled to a deep change in the bacterial community diversity and structure of the granular biomass. Azithromycin, norfloxacin and trimethoprim were efficiently removed in the CANON bioreactor, reducing its concentration 77.9 ± 11.2%, 51.7 ± 10.7% and 57.8 ± 8.1%, respectively. The granular biomass changed significantly with the addition of the antibiotics, decreasing in settling velocity but increasing in compactness, losing its inner porous structure but developing a protective outer layer build of cell material. Prolonged operation under the antibiotics loading promoted the adaptation of multi-drug resistant fungus Scedosporium boydii fungal species and of Acidovorax ebreus TPSY, Alcaligenes aquatilis, Paracoccus versutus or Ochrobactrum antropii, which have been identified as human, animal and/or plant pathogens.