Flows in microcapillaries and associated imbibition phenomena play a major role across a wide spectrum of practical applications, from oil recovery to inkjet printing and from absorption in porous materials and water transport in trees to biofluidic phenomena in biomedical devices. Early investigations of spontaneous imbibition in capillaries led to the observation of a universal scaling behavior, known as the Lucas-Washburn (LW) law. The LW allows abstraction of many real-life effects, such as the inertia of the fluid, irregularities in the wall geometry, and the finite density of the vacuum phase (gas or vapor) within the channel. Such simplifying assumptions set a constraint on the design of modern microfluidic devices, operating at ever-decreasing space and time scales, where the aforementioned simplifications go under serious question. Here, through a combined use of leading-edge experimental and simulation techniques, we unravel a novel interplay between global shape and nanoscopic roughness. This interplay significantly affects the early-stage energy budget, controlling front propagation in corrugated microchannels. We find that such a budget is governed by a two-scale phenomenon: The global geometry sets the conditions for small-scale structures to develop and propagate ahead of the main front. These small-scale structures probe the fine-scale details of the wall geometry (nanocorrugations), and the additional friction they experience slows the entire front. We speculate that such a two-scale mechanism may provide a fairly general scenario to account for extra dissipative phenomena occurring in capillary flows with nanocorrugated walls.