Dipeptides can be self-assembled via non-covalent bonds towards functional nanostructures for diverse applications in nanotechnology. Here, we introduce a convenient microfluidics-guided dipeptide design as a platform for photodegradation of contaminants in water. Titanium dioxide (TiO₂) nanoparticles (NPs) are chosen as photocatalysts due to their vastly studied properties. By using a well-defined microchannel architecture, the dipeptide N-fluorenylmethoxycarbonyl diphenylalanine (Fmoc-FF) and TiO₂ NPs are efficiently mixed leading to a self-assembled Fmoc-FF hydrogel with embedded TiO₂. Owing to shear-thinning and rapid self-healing of Fmoc-FF hydrogels, we can transfer and inject Fmoc-FF/TiO₂ hydrogels into any other microdevice for specific applications, where these low-molecular-weight-gelator- (LMWG-)based Fmoc-FF hydrogels fill out the microchannel volume. Different morphologies of Fmoc-FF/TiO₂ hydrogels are obtained by simple concentration screening of TiO₂ NPs and Fmoc-FF. Owing to the density of the three-dimensionally twined Fmoc-FF nanofibers, solutions swelling the dipeptide hydrogel can be exchanged without leaching out TiO₂ NPs. By further analysis, our hydrogel-filled flow cell can be employed for continuous-flow photodegradation in water under light irradiation. Especially, compared to the TiO₂ NPs suspension, Fmoc-FF/TiO₂ hydrogels with relatively low concentrations of TiO₂ exhibit enhanced photodegradation capabilities due to better dispersion of nanoparticles. Such strategy provides a versatile platform for embedment of small inorganic catalysts or enzymes for (bio-)chemical conversion of solutes passing through the hydrogel network.