Mitochondria are involved in numerous processes vital for cellular homeostasis, therefore, mitochondrial dysfunction can lead to a wide range of diseases. Understanding mitochondrial function in health and disease is crucial for the development of efficient therapies, for which targeting bioactive compounds to mitochondria is a promising strategy. The best characterised approach is to attach the bioactive moiety to a triphenylphosphonium cation (TPP), which drives membrane potential-dependent uptake into the organelle. However, there are still limitations associated with TPP-targeting, some of which I have attempted to overcome in this work. Firstly, I have investigated the use of labile linkers to connect bioactive moieties to the TPP cation, allowing their release from TPP once they are taken up by mitochondria. This strategy could allow the lock-in of compounds within mitochondria, a feature that is currently not routinely possible. Furthermore, this approach could minimise negative effects the TPP cation could have on the compound’s bioactivity. In order to select linker candidates, I have performed a bioinformatics analysis to investigate which structures are enzymatically cleaved inside mitochondria but are stable when crossing the plasma membrane and the cytosol. Then, I developed a fast screening method using coumarin fluorescence to test the stability of these candidates across multiple conditions. I have also tested the use of an ester bond to deliver a hydrophobic compound (an analogue of MitoQ10) to mitochondria, as well as the use of a cleavable mask to deliver a polar compound (a phosphate group which is charged at physiological pH). I have also addressed the lack of probes to measure mitochondrial membrane potential that could be used in vivo in live models, without the need for tissue homogenization. For that I used click chemistry with the goal of targeting two TPP precursors that would react inside mitochondria to generate labelled N2, which could then be detected externally in the expired gases. Finally, I have investigated whether TPP dications could be used to improve the uptake and retention of a hydrogen peroxide probe, MitoB, in cells and in vivo. These approaches have provided a number of insights into how to develop new mitochondria targeted compounds.