The observed quarkonia states in heavy ion collisions provide a powerful tool to probe the dynamics of the Quark Gluon Plasma. Measurements performed on the ground and excited quarkonia states, as well as their separation into prompt and non-prompt components, reveal the effects of colour screening and colour recombination. In addition, quarkonium production rates and their excited to ground state production ratios in lighter p+Pb collisions are an interesting probe of cold nuclear matter effects. In these proceedings, the latest results of the ATLAS experiment at the LHC on these observables will be presented.