The extremely high levels of water pollution caused by various industrial activities represent one of the most important environmental problems. Efficient techniques and advanced materials have been extensively developed for the removal of highly toxic organic pollutants, including pesticides. This study investigated the photocatalytic degradation of the fungicide carbendazim (Czm) using composite track-etched membranes (TeMs) in an aqueous solution. Copper(I) oxide (Cu2O) and zinc oxide (ZnO) microtubes (MTs) were prepared using an electroless template deposition technique in porous poly(ethylene terephthalate) (PET) TeMs with nanochannels with a density of 4 × 107 pores/cm−2 and diameter of 385 ± 9 nm to yield Cu2O@PET and ZnO@PET composite membranes, respectively. A mixed Cu2O/ZnO@PET composite was prepared via a two-step deposition process, containing ZnO (87%) and CuZ (13%) as crystalline phases. The structure and composition of all composite membranes were elucidated using scanning electron microscopy (SEM), atomic force microscopy (AFM), energy-dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD) techniques. Under UV–visible light irradiation, the Cu2O/ZnO@PET composite displayed enhanced photocatalytic activity, reaching 98% Czm degradation, higher than Cu2O@PET and ZnO@PET composites. The maximum Czm degradation efficiency from aqueous solution was obtained at an optimal pH of 6 and contact time of 140 min. The effects of various parameters such as temperature, catalyst dosage and sample exposure time on the photocatalytic degradation process were studied. The degradation reaction of Czm was found to follow the Langmuir–Hinshelwood mechanism and a pseudo-first order kinetic model. The degradation kinetics of Czm accelerated with increasing temperature, and the activation energy (Ea) levels were calculated as 11.9 kJ/mol, 14.22 kJ/mol and 15.82 kJ/mol for Cu2O/ZnO@PET, ZnO@PET and Cu2O@PET composite membranes, respectively. The reusability of the Cu2O/ZnO@PET catalyst was also investigated at different temperatures for 10 consecutive runs, without any activation or regeneration processes. The Cu2O/ZnO@PET composite exhibited degradation efficiency levels of over 50% at 14 °C and over 30% at 52 °C after 5 consecutive uses.