AbstractSolid-state spin qubits is a promising platform for quantum computation and quantum networks1,2. Recent experiments have demonstrated high-quality control over multi-qubit systems3–8, elementary quantum algorithms8–11 and non-fault-tolerant error correction12–14. Large-scale systems will require using error-corrected logical qubits that are operated fault tolerantly, so that reliable computation becomes possible despite noisy operations15–18. Overcoming imperfections in this way remains an important outstanding challenge for quantum science15,19–27. Here, we demonstrate fault-tolerant operations on a logical qubit using spin qubits in diamond. Our approach is based on the five-qubit code with a recently discovered flag protocol that enables fault tolerance using a total of seven qubits28–30. We encode the logical qubit using a new protocol based on repeated multi-qubit measurements and show that it outperforms non-fault-tolerant encoding schemes. We then fault-tolerantly manipulate the logical qubit through a complete set of single-qubit Clifford gates. Finally, we demonstrate flagged stabilizer measurements with real-time processing of the outcomes. Such measurements are a primitive for fault-tolerant quantum error correction. Although future improvements in fidelity and the number of qubits will be required to suppress logical error rates below the physical error rates, our realization of fault-tolerant protocols on the logical-qubit level is a key step towards quantum information processing based on solid-state spins.