Programmability is increasingly central in emerging quantum network software stacks, yet the node-internal controller-to-hardware interface for quantum repeater devices remains under-specified. We introduce the idea of an instruction-set architecture (ISA) for controller-driven programmability of nitrogen-vacancy (NV) center quantum repeater nodes. Each node consists of an optically interfaced electron spin acting as a data qubit and a long-lived nuclear-spin register acting as a control program. We formalize two modes of programmability: (i) deterministic register control, where the nuclear register is initialized in a basis state to select a specific operation on the data qubit; and (ii) coherent register control, where the register is prepared in superposition, enabling coherent combinations of operations beyond classical programmability. Network protocols are expressed as controller-issued instruction vectors, which we illustrate through a compact realization of the BBPSSW purification protocol. We further show that coherent register control enables interferometric diagnostics such as fidelity witnessing and calibration, providing tools unavailable in classical programmability. Finally, we discuss scalability to multi-electron and multi-nuclear spin architectures and connection to Linear combination of unitaries (LCU) and Kraus formulation.