We present cosmological, radiation-hydrodynamics simulations of galaxy formation during the epoch of reionization in an effort towards modelling the interstellar medium (ISM) and interpreting Atacama Large Millimeter Array (ALMA) observations. Simulations with and without stellar radiation are compared at large (Mpc), intermediate (tens of kpc) and small (sub-kpc) scales. At large scales, the dense regions around galaxies reionize first before ultraviolet (UV) photons penetrate the voids; however, considerable amounts of neutral gas remain present within the haloes. The spatial distribution of neutral gas is highly dynamic and is anticorrelated with the presence of stars older than a few Myr. For our specific feedback implementation, most of the metals remain inside the virial radii of haloes, and they are proportionally distributed over the ionized and neutral media by mass. For our most massive galaxy with Mh ∼ 10$\mathrm{<mrow\; data-mjx-texclass="ORD">11</mrow>}$ M⊙, the majority of the C ii and O i masses are associated with cold neutral clumps. N ii is more diffuse and arises in warmer gas, while O iii arises in hotter gas with a higher ionization parameter, produced by photoheating and supernovae. If smaller pockets of high-metallicity gas exist in the ISM, the emission from these ions may be observable by ALMA, while the low metallicity of the galaxy may cause these systems to fall below the local [C ii]–star formation rate relation. The presence of dust can cause spatial offsets between UV/Lyman α and [C ii] emissions, as suggested by the recent observations of Maiolino et al. [O iii] may be spatially offset from both of these components since it arises from a different part of density–temperature phase space.