Filamentous fungi Trichoderma have been able to efficiently degrade fluoroquinolone antibiotics namely ciprofloxacin (CIP) and ofloxacin (OFL) as well as the fungicide climbazole (CLB) that are persistent in conventional activated sludge processes. All targeted compounds were biotransformed by whole cells of Trichoderma spp., exactly T. harzanium and T. asperellum, and biosorption played a limited role in their elimination. However, contrasting results were obtained with the two strains. T. asperellum was more efficient against CIP, with a 81% degradation rate in 13 days of incubation, while T. harzianum was more efficient against CLB, with a 91% degradation rate. While in the case of OFL, both strains showed same efficiency with degradation rate around 40%. Adding a cytochrome P450 enzyme inhibitor hardly resulted in the modification of degradation kinetics supporting the implication of extracellular enzymes in chemical biotransformation. Transformation products were identified by liquid chromatography-high resolution-mass spectrometry and transformation pathways were proposed. Biotransformation of selected compounds included hydroxylation, oxidation/reduction and N- and O-dealkylation reactions, similarly to those reported with white rot fungi. CIP underwent transformations at the piperazinyl ring through oxidation and conjugation reactions, while OFL mainly underwent hydroxylation processes and CLB carbonyl reduction into alcohol. Consequently, Trichoderma spp. likely possess a machinery of unspecific enzymes, which makes their application in removal of pharmaceutical and personal care products attractive.