We study the transition probabilities of a two-point measurement on a quantum system, initially prepared in a thermal state. We find two independent constraints on the difference between transition probabilities when the system is prepared at different temperatures, which both turn out to be particularly restrictive when the measured quantum system is small. These bounds take the form of a thermodynamic and of an energetic constraint because they are associated with the dissipated heat and with the absorbed energy required to increase or to reduce the temperature of the system. The derived constraints apply to arbitrary system Hamiltonians, including interactions or nonlinear energy spectra. We show the relevance of these constraints for the special case where transitions are induced by energy or particle exchange in weakly coupled bipartite systems out of equilibrium. This example is of interest for a wide range of experimentally relevant systems, from molecular junctions to coupled cavities, and can be tested by, for instance, measuring the out-of-equilibrium tunneling current and its noise.