Galaxies at high redshifts with strong star formation are sources of high-energy cosmic rays. These cosmic rays interact with the baryon and radiation fields of the galactic environment via photo-pair, photo-pion and proton-proton processes to produce charged and neutral pions, neutrons and protons. The cosmic rays thereby deposit energy into the interstellar medium (ISM) as they propagate. We show how energy transport and deposition by ultra high-energy cosmic rays is regulated by the evolution of the galaxy, in particular by the development of the galactic magnetic field. We show how the particle-driven energy deposition can influence the thermal evolution of the host and its surroundings. Using a parametric protogalaxy model, we calculate the heating effect on the ISM as the cosmic rays are increasingly confined by the magnetic evolution of the galaxy.