The role of mitochondria in Ca2+ handling has acquired renewed interest in recent years in the field of cell signaling. Detailed studies of Ca2+ dynamics in this organelle at the single cell level have been hampered by technical problems in the available Ca2+ probes. Some of the latest generation GFP-based Ca2+ probes (Camgaroos, Cameleons and Pericams) show great potential to address this issue. Our data show that the choice of targeting sequence influences not only the overall efficiency of subcellular localization of the probes, but also their functional characteristics within the matrix. In particular, we here show that the use of a tandemly duplicated mitochondrial targeting sequence is capable of improving the delivery efficacy of all tested probes into the organelle's matrix, in particular that of Cameleon, a GFP-based Ca2+ probe that is otherwise largely mistargeted to the cytosol. The devised strategy should be generally applicable to other proteins that are characterized by poor targeting. Last, but not least, we also demonstrate that if the targeting sequence is not removed from the imported protein, the fluorescent properties and the Ca2+ affinity of the probe can be grossly affected.