The origin of cosmic-rays remains one of the most important open questions in astrophysics. A powerful tool to study their acceleration sites are multi-messenger (photons and neutrinos) observations: wherever a cosmic-ray (a proton or an atomic nucleus) is accelerated, it interacts with its environment producing pions that then decay into photons, neutrinos and electrons. γ and ν can escape the region and travel on geodesics to Earth, pinpointing their source in the Universe.