We discuss the role of quantum coherence in the energy fluctuations of open quantum systems. To this aim, we introduce an operational protocol, to which we refer to as the end-point-measurement scheme, allowing to define the statistics of energy changes as a function of energy measurements performed only after its evolution. At the price of an additional uncertainty on the value of the initial energies, this approach prevents the loss of initial quantum coherences and enables the estimation of their effects on energy fluctuations. We illustrate our findings using a three-level quantum system in interaction with thermal reservoirs.