Phosphonium-based ionic conjugates (PBICs) are described. The PBICs each include a cationic binding partner comprising a phosphonium ion and an anionic binding partner comprising a pharmaceutically active compound, or prodrug, or derivative thereof. The conjugate can have at least one enhanced physiochemical, pharmacokinetic and/or therapeutic quality as compared to the pharmaceutically active compound when not provided in a PBIC. The phosphonium-containing cationic binding partner can also serve to enhance delivery of the anionic binding partner to the cytosol and/or the inner mitochondrial space. Methods of preparing the PBICs and using the PBICs to treat disease are also described.