We present CO(1-0) and CO(3-2) Atacama Large Millimeter/submillimeter Array observations of the molecular gas in PKS 1549-79, as well as mm and very long baseline interferometry 2.3-GHz continuum observations of its radio jet. PKS 1549-79 is one of the closest young, radio-loud quasars caught in an on-going merger in which the active galactic nucleus (AGN) is in the first phases of its evolution. We detect three structures tracing the accretion and the outflow of molecular gas: kpc- scale tails of gas accreting onto PKS 1549-79 from a merger, a circumnuclear disc in the inner few hundred parsec, and a very broad (> 2300 km s-1) component detected in CO(1-0) at the position of the AGN. Thus, in PKS 1549-79 we see the co-existence of accre...