We apply estimation theory to a system formed by two interacting trapped ions. By using the Fisher matrix formalism, we introduce a simple scheme for estimation of the temperature of the longitudinal vibrational modes of the ions. We use the ions interaction to effectively infer the temperature of the individual ions, by optimising the interaction time evolution and by measuring only over one of the ions. We also investigate the effect of a non-thermal reservoir over the inference approach. The non-classicality of one of the ions vibrational modes, introduced due to a squeezed thermal reservoir, improves the indirect inference of the individual temperatures.