Self-assembly and on-surface synthesis are vital strategies used for fabricating surface-confined 1D or 2D supramolecular nanoarchitectures with atomic precision. In many systems, the resulting structure is determined by kinetics of processes involved, i.e., reaction rate, on-surface diffusion, nucleation, and growth, all of which are typically governed by temperature. However, other external factors have been only scarcely harnessed to control the on-surface chemical reaction kinetics and self-assembly. Here, we show that a low-energy electron beam can be used to steer chemical reaction kinetics and induce the growth of molecular phases unattainable by thermal annealing. The electron beam provides a well-controlled means of promoting the elementary reaction step, i.e., deprotonation of carboxyl groups. The reaction rate linearly increases with increasing electron beam energy beyond the threshold energy of 6 eV. Our results offer the novel prospect of controlling the self-assembly, enhancing the rate of reaction steps selectively, and thus altering the kinetic rate hierarchy.