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Anaerobic bioreactors are an efficient technology for the biodegradation of emerging contaminants in environmental matrices. In this work, a horizontal-flow anaerobic immobilized biomass (HAIB) bioreactor was used to remove caffeine (CAF), which is frequently found in various aqueous matrices. The acrylic bench top bioreactor, with dimensions of 100 × 5.00 cm, was operated with a hydraulic retention time (HRT) of 12 h, during 45 weeks, under mesophilic conditions. The operation was performed in 4 phases: without CAF addition (phase I); CAF spiked at 300 μg L -1 (phase II); CAF at 600 μg L -1 (phase III); and CAF at 900 μg L -1 (phase IV). Samples of bioreactor influent and effluent were analyzed by liquid chromatography/tandem mass spectrometry (LC-MS/MS). The bioreactor removed organic matter (OM) and CAF with efficiencies of 88 and 93%, respectively. The first-order apparent removal constant (K app ) values for OM and CAF were 0.419 and 0.304 h -1 , respectively. Five transformation products (TPs) were identified, with m/z 243, 227, 211, and 181 (two products). The HAIB bioreactor is a suitable system for the removal of CAF present in wastewater, even at a concentration level of µg L -1 ., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)