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 PKS1549-79 from a merger, a circumnuclear disc in the inner few hundred parsec, and a very broad (>2300km/s) component detected in CO(1-0) at the position of the AGN. Thus, in PKS 1549-79 we see the co-existence of accretion and the ejection of gas. The line ratio CO(3-2)/CO(1-0) suggests that the gas in the circumnuclear-disc has both high densities and high kinetic temperatures. We estimate a mass outflow rate of at least 650M_{sun}_/yr. This massive outflow is confined to the inner region (r<120pc) of the galaxy, which suggests that the AGN drives the outflow. Considering the amount of molecular gas available in the central nuclear disc and the observed outflow rate, we estimate a time scale of 10^5^yr over which the AGN would be able to destroy the circumnuclear disc, although gas from the merger may come in from larger radii, rebuilding this disc at the same time. The AGN appears to self-regulate gas accretion to the centre and onto the super-massive black hole. Surprisingly, from a comparison with Hubble Space Telescope data, we find that the ionised gas outflow is more extended. Nevertheless, the warm outflow is about two orders of magnitude less massive than the molecular outflow. PKS 1549-79 does not seem to follow the scaling relation between bolometric luminosity and the relative importance of warm ionised and molecular outflows claimed to exist for other AGN. We argue that, although PKS 1549-79 hosts a powerful quasar nucleus and an ultra-fast outflow, the radio jet plays a significant role in producing the outflow, which creates a cocoon of disturbed gas that expands into the circumnuclear disc.

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