Advanced oxidation processes, including photocatalysis, have been proven effective at organic dye degradation. Tailored porous materials with regulated pore size, shape, and morphology offer a sustainable solution to the water pollution problem by acting as support materials to grafted photocatalytic nanoparticles (NPs). This research investigated the influence of pore and particle sizes of photocatalytic MICROSCAFS® on the degradation of methyl orange (MO) in aqueous solution (10 mg/L). Photocatalytic MICROSCAFS® are made of binder-less supported P25 TiO2 NPs within MICROSCAFS®, which are silica–titania microspheres with a controlled size and interconnected macroporosity, synthesized by an adapted sol–gel method that involves a polymerization-induced phase separation process. Photocatalytic experiments were performed both in batch and flow reactors, with this latter one targeting a proof of concept for continuous transformation processes and real-life conditions. Photocatalytic degradation of 87% in 2 h (batch) was achieved, using a calibrated solar light simulator (1 sun) and a photocatalyst/pollutant mass ratio of 23. This study introduces a novel flow kinetic model which provides the modeling and simulation of the photocatalytic MICROSCAFS® performance. A scavenger study was performed, enabling an in-depth mechanistic understanding. Finally, the transformation products resulting from the MO photocatalytic degradation were elucidated by high-resolution mass spectrometry experiments and subjected to an in silico toxicity assessment.