By combining ab initio time-dependent density functional calculations for electrons with molecular dynamics simulations for ions in real time, we investigate the microscopic mechanism of collisions between energetic protons and graphitic carbon nanostructures. We identify not only the amount of energy lost by the projectile, but also the electronic and ionic degrees of freedom of the target that accommodate this energy as a function of the impact parameter and projectile energy. Our results establish validity limits for the Born-Oppenheimer approximation and the threshold energy for defect formation in carbon nanostructures.