Visible-light driven photocatalysts are of great importance in wastewater treatment. In this work, fluorine and nitrogen co-doped titanium dioxide/silica nanocomposite (F–N–TiO2/SiO2) was synthetized using a sol-gel approach. The as-developed nanocomposite was well characterized using different techniques. In particular, an anatase structure with high surface area (345.69 m2/g) and a band gap of 2.97 eV were observed for the as-synthesized nanocomposite, which makes it a potential candidate for photocatalytic applications under visible light. A systematic density functional theory calculation was performed to get more insight into the effect of dopant atoms on the band gap of TiO2 nanoparticles. To enhance the reusability of the photocatalyst in semi-pilot scale, the as-developed nanocomposite was immobilized onto the glass beads by coupling dip-coating and heat attachment methods. A semi-pilot scale custom-designed fixed-bed photoreactor was used to evaluate the photocatalytic performance of the as-developed nanocomposite under both visible and solar irradiations. A mixture of three azo dyes (i.e., basic red 29, basic blue 41 and basic yellow 51) was used as the model industrial wastewater. The analysis of the wastewater showed that the complete removal of the pollutants under visible light and sunlight can occurred at pH of 3 and flow rate of 280 mL/min. The durability results demonstrated the successful degradation of the pollutants for five cycles. The results of this study show how careful controlling the operational parameters as well as using a highly photocatalytic nanomaterial can lead to successful decontamination of organic water pollutants. This approach might open up new windows to the future applications of photocatalytic nanomaterials for wastewater treatment.