Nuclear spins were among the first physical platforms to be considered for quantum information processing, because of their exceptional quantum coherence and atomic-scale footprint. However, their full potential for quantum computing has not yet been realized, due to the lack of methods to link nuclear qubits within a scalable device combined with multi-qubit operations with sufficient fidelity to sustain fault-tolerant quantum computation. Here we demonstrate universal quantum logic operations using a pair of ion-implanted $^{31}$P nuclei in a silicon nanoelectronic device. A nuclear two-qubit controlled-Z gate is obtained by imparting a geometric phase to a shared electron spin, and used to prepare entangled Bell states with fidelities up to 94.2(2.7)%. The quantum operations are precisely characterised using gate set tomography (GST), yielding one-qubit gate fidelities up to 99.93(3)%, two-qubit gate fidelity of 99.21(14)% and two-qubit preparation/measurement fidelities of 98.95(4)%. These three metrics indicate that nuclear spins in silicon are approaching the performance demanded in fault-tolerant quantum processors. We then demonstrate entanglement between the two nuclei and the shared electron by producing a Greenberger-Horne-Zeilinger three-qubit state with 92.5(1.0)% fidelity. Since electron spin qubits in semiconductors can be further coupled to other electrons or physically shuttled across different locations, these results establish a viable route for scalable quantum information processing using nuclear spins.
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