Targeted drug delivery is an established strategy in medicinal chemistry, aiming to achieve the selective distribution of a substance, increasing its accumulations in pre-designated organs, cells, or specific organelles. Its main advantage is probably the ability to reduce the amount of substance needed to achieve an effect, which in itself leads to reduction in unwanted side effects. Despite being extensively used in other fields, targeting has not been thoroughly tested in plants. This approach can benefit both basic plant research and agricultural practices. Targeted delivery can be applied to various plant species and can be used to study plants with minimum genetic interference to the organism. Additionally, small molecules, such as hormones or inhibitors, could be directed to specific locations, enabling them to dissect their functions at a much higher resolution. Herein, we explore the utility of triphenylphosphonium (TPP), a mitochondria targeting moiety, as the first step of targeted delivery in plants. TPP had been vastly used in mammalian cells. Using fluorescently labeled TPP derivatives, we show that TPP exclusively accumulates in Arabidopsis thaliana mitochondria in vitro and in planta. Furthermore, TPP was conjugated with the DNA stain Hoechst, demonstrating its ability to shift from accumulating in nuclei to accumulating in mitochondria. Another molecule was the antibiotic ciprofloxacin (CFX), a DNA gyrase inhibitor. Previous studies showed plant gyrase exists both in mitochondria and chloroplasts of plants. By targeting ciprofloxacin to the mitochondria, we can uncouple its activities in the different organelles, providing a higher resolution for understanding this enzyme`s functions.