Nucleoside diphosphates and triphosphates impact nearly every aspect of biochemistry, however, the use of such compounds as tools or medicinal leads for nucleotide-dependent enzymes and receptors is hampered due to rapid metabolism. Meanwhile, a successful strategy to address the instability of the monophosphate moiety in oligonucleotide therapeutics has been accomplished by their isosteric replacement with phosphorothioates. On the contrary, no practical methods exist to rapidly and controllably access stereopure di- and triphosphate thioisosteres of both natural and unnatural nucleosides. Here we show how a modular, reagent-based platform can enable the stereocontrolled and scalable synthesis of a library of such molecules. Such thioisosteric replacements can have profound effects on the potency and stability of lead candidates, as evidenced by data demonstrating that ligand-receptor interactions can be dramatically influenced by P-stereochemistry.