The generation of pH-sensitive fluorescent probes to monitor autophagy has greatly advanced our understanding of autophagic flux. In particular, genetically encoding these probes within model organisms has expanded our appreciation of the complexities of physiological autophagy. Reporter probes localize to distinct cellular components, allowing tractable and robust monitoring of general or specific autophagy pathways. Though the principle upon which they operate is similar, each reporter system exhibits subtle differences in the information they report. As with every tool or reagent, each has inherent advantages and disadvantages. These differences are a function of the composition and configuration of each probe, such as the type of fluorescent protein used or the mode in which they localize to a specific organelle. Here, we would like to comment on a recent article comparing the mitophagy reporters mt-Keima and mito-QC.