The occurrence of a range of recalcitrant organic micropollutants in our aquatic environment has led to the development of various tertiary wastewater treatment methods. In this study, biogenic manganese oxides (Bio-MnOx), biogenic silver nanoparticles (Bio-Ag0) and ionic silver were used for the oxidative removal of the frequently encountered drug diclofenac and its dechlorinated form, 2-anilinophenylacetate (APA). Diclofenac was rapidly degraded during ongoing manganese oxidation by Pseudomonas putida MnB6. Furthermore, whereas preoxidized Bio-MnOx, Bio-Ag0 and Ag+ separately did not show any removal capacity for diclofenac, an enhanced removal occurred when Bio-MnOx and silver species were combined. Similar results were obtained for APA. Finally, a slow removal of diclofenac but more rapid APA degradation was observed when silver was added to manganese-free P. putida biomass. Combining these results, three mechanisms of diclofenac and APA removal could be distinguished: (i) a co-metabolic removal during active Mn2+ oxidation by P. putida; (ii) a synergistic interaction between preoxidized Bio-MnOx and silver species; and (iii) a (bio)chemical process by biomass enriched with silver catalysts. This paper demonstrates the use of P. putida for water treatment purposes and is the first report of the application of silver combined with biogenic manganese for the removal of organic water contaminants.