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Abstract Building on a general relativistic magnetohydrodynamic simulation of a short gamma-ray burst (sGRB) jet with initial magnetizationσ₀ = 150, propagating through the dynamical ejecta from a binary neutron star merger, we identify regions of energy dissipation driven by magnetic reconnection and collisionless subshocks within different scenarios. We solve the transport equations for photons, electrons, protons, neutrinos, and intermediate particles up to the photosphere, accounting for all relevant radiative processes, including electron and proton acceleration, and investigate the potential impact of magnetic reconnection occurring in different regions along the jet. We find the photon spectra undergo nonthermal modifications below the photosphere, observable in both on-axis and off-axis emission directions, as well as across different scenarios of energy dissipation and subsequent particle acceleration. Interestingly, the spectral index of the photon energy distribution can vary at most by ∼20% across all different dissipation scenarios. Depending on the dissipation mechanism at play, neutrino signatures may accompany the photon signal, pointing to efficient proton acceleration and shedding light on jet physics. Although our findings are based on one jet simulation, they point to a potential universal origin of the nonthermal features of the Band spectrum observed in sGRBs.