Efficient hydrogelators will gel water fast and at low concentrations. Small molecule gelling agents that assemble into fibers and fiber networks are particularly effective hydrogelators. Whereas it is straightforward to determine their critical concentration for hydrogelation, the kinetics of hydrogelation is more difficult to study because it is often very fast, occurring on the subsecond time scale. We used a 3D focusing microfluidic device combined with fluorescence microscopy and in situ small-angle X-ray scattering (SAXS) to study the fast pH-induced gelation of a model small molecule gelling agent at the millisecond time scale. The gelator is a 1,3,S-benzene tricarboxamide which upon acidification assembles into nanofibrils and fibril networks that show a characteristic photoluminescence. By adjusting the flow rates, the regime of early nanofibril formation and gelation could be followed along the microfluidic reaction channel. The measured fluorescence intensity profiles were analyzed in terms of a diffusion-advection-reaction model to determine the association rate constant, which is in a typical range for the small molecule self-assembly. Using in situ SAXS, we could determine the dimensions of the fibers that were formed during the early self assembly process. The detailed structure of the fibers was subsequently determined by cryotransmission electron microscopy. The study demonstrates that 3D focusing microfluidic devices are a powerful means to study the self-assembly on the millisecond time scale, which is applied to reveal early state of hydrogelation kinetics. In combination with in situ fluorescence and X-ray scattering, these experiments provide detailed insights into the first self-assembly steps and their reaction rates.