The main objective of this research is to perform a real case-study of antibiotic decontamination from real slaughterhouse and wastewater effluents by applying a sequential treatment of TiO2/UV–vis photocatalysis and adsorption. More precisely, the removal of five classes of antibiotics: enrofloxacin, sulfadiazine, trimethoprim, azithromycin, amoxicillin and amoxicillin degradation products was studied in an 80 L/h photocatalytic and adsorption pilot-scale plant over multiple cycles, operating in semi-continuous mode. The results exhibited significant removal rates, ranging from 77% to 100% for the slaughterhouse effluent, and 61–89% for the wastewater treatment plant effluent, thus demonstrating that the treatment is more effective when it is applied directly in the emission source, previous to antibiotic dilution in the municipal collector. Using the two processes sequentially results in greater efficiency than when they are used in isolation. After photocatalysis, antibiotic degradation products are easily adsorbed, since they have more affinity for the adsorbent, and the presence of competing compounds decreases considerably. After applying several cycles of treatment, the adsorption performance remains almost constant. By contrast, the photocatalysis performance decreased, which was attributed to catalyst agglomeration determined by Asymmetric Flow Field-Flow Fractionation (AF4) coupled with Dynamic Light Scattering (DLS) and Inductively Coupled Plasma Mass Spectrometry (ICP-MS).