The far infrared physics is a fascinating topic for theoretical physics, since the foundation of quantum field theory and neutrinos seem to be strongly related with the far infrared physics of our Universe. In this work we shall explore the possibility of a late-time thermal phase transition caused by the axion–neutrino interactions. The axion is assumed to be the misalignment axion which is coupled primordially to a chiral symmetric neutrino. The chiral symmetry is supposed to be broken either spontaneously or explicitly, and two distinct phenomenological models of axion–neutrinos are constructed. The axion behaves as cold dark matter during all its evolution eras, however if we assume that the axion and the neutrino fields interact coherently in a classical way as fields, or as ensembles, then we consider thermal effects in the axion sector, due to the values of operators ϕ for the axion and ν̄ν due to the neutrinos. The thermal equilibrium between the two has no effect to the axion effective potential for a wide temperature range. As we show, contrary to the existing literature, the axion never becomes destabilized due to the finite temperature effects, however if axion-Higgs higher order non-renormalizable operators are present in the Lagrangian, the axion potential is destabilized in the temperature range T∼0.1MeV down to T∼0.01eV and a first order phase transition takes place. The initial axion vacuum decays to the energetically more favorable axion vacuum, and the latter decays to the Higgs vacuum which is more preferable. This late-time phase transition might take place in the redshift range z∼385−37 and thus it may cause density fluctuations in the post-recombination era. This might be the source of large scale matter structure at high redshifts z≥9. Following the literature, we qualitatively discuss the implications of such a late-time phase transition at the astrophysical and cosmological level.