The main signature of the interaction between cosmic rays and molecular clouds is the high ionisation degree. This decreases towards the densest parts of a cloud, where star formation is expected, because of energy losses and magnetic effects. However recent observations hint to high levels of ionisation in protostellar systems, therefore leading to an apparent contradiction that could be explained by the presence of energetic particles accelerated within young protostars. Our modelling consists of a set of conditions that has to be satisfied in order to have an efficient particle acceleration through the diffusive shock acceleration mechanism. We find that jet shocks can be strong accelerators of protons which can be boosted up to relativistic energies. Another possibly efficient acceleration site is located at protostellar surfaces, where shocks caused by impacting material during the collapse phase are strong enough to accelerate protons. Our results demonstrate the possibility of accelerating particles during the early phase of a proto-Solar-like system and can be used as an argument to support available observations. The existence of an internal source of energetic particles can have a strong and unforeseen impact on the star and planet formation process as well as on the formation of pre-biotic molecules.