Photocatalysis is a prominent alternative wastewater treatment technique that has the potential to completely degrade pesticides as well as other persistent organic pollutants, leading to detoxification of wastewater and thus paving the way for its efficient reuse. In addition to the more conventional photocatalysts (e.g., TiO2, ZnO, etc.) that utilize only UV light for activation, the interest of the scientific community has recently focused on the development and application of visible light-activated photocatalysts like g-C3N4. However, some disadvantages of g-C3N4, such as the high recombination rate of photogenerated charges, limit its utility. In this light, the present study focuses on the synthesis of WO3 fibers/g-C3N4 Z-scheme heterojunctions to improve the efficiency of g-C3N4 towards the photocatalytic removal of the widely used insecticide clothianidin. The effect of two different g-C3N4 precursors (urea and thiourea) and of WO3 fiber content on the properties of the synthesized composite materials was also investigated. All aforementioned materials were characterized by a number of techniques (XRD, SEM-EDS, ATR-FTIR, Raman spectroscopy, DRS, etc.). According to the results, mixing 6.5% W/W WO3 fibers with either urea or thiourea derived g-C3N4 significantly increased the photocatalytic activity of the resulting composites compared to the precursor materials. In order to further elucidate the effect of the most efficient composite photocatalyst in the degradation of clothianidin, the generated transformation products were tentatively identified through UHPLC tandem high-resolution mass spectroscopy. Finally, the detoxification effect of the most efficient process was also assessed by combining the results of an in-vitro methodology and the predictions of two in-silico tools.