Determination of the gas temperature in the afterglow plasma jet of pre-cooled helium propagating inside a dense helium vapor at 1.4 K is a difficult task. In this work we analyze the possibility of using the emission spectra from oxygen atoms and nitrogen molecules for deducing the local temperature of the gas. Oxygen is always present as a trace impurity (∼1 ppm) in helium gas and strong emission of the atomic 777 nm triplet lines can be a good candidate because the energy gaps of 3.67 cm−1 (T ∼ 5.3 K) and 2.02 cm−1 (T ∼ 2.9 K) between the sub-levels of its upper state O(5P J ), with J = 1, 2 and 3, are comparable to the kinetic energy of atoms in a cryogenic environment. A detailed analysis of the kinetics of atoms in the O(5P J ) state indicates that at temperatures lower than 10 K, the population transfers between sub-levels are not efficient enough for the establishment of a Boltzmann equilibrium within the sublevels before the radiative decay of O(5P J ) atoms. We suggest the presence of small energy barriers in the He-O(5P J ) transient molecule formed during the collision. It was also shown that the temperature of a gas in non-equilibrium cryogenic helium plasmas containing at least 100 ppm of nitrogen can be determined from the rotational spectra of the 2–0 and 3–1 bands of the first positive system and the 8–3 band of the infrared afterglow system of molecular nitrogen. The application of PGOPHER software (1-T method) gives the rotational temperature of N2 molecules averaged over the observation area and is optimal for the gas temperature determination in locally homogeneous plasmas or mapping the temperature in inhomogeneous plasmas with high spatial resolution. A home-made code to simulate rotational spectra with two temperatures (2-T method) allows determination of the temperature span within the observation region of an inhomogeneous plasma.