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Suppressing errors is the central challenge for useful quantum computing1, requiring quantum error correction (QEC)2–6for large-scale processing. However, the overhead in the realization of error-corrected ‘logical’ qubits, in which information is encoded across many physical qubits for redundancy2–4, poses substantial challenges to large-scale logical quantum computing. Here we report the realization of a programmable quantum processor based on encoded logical qubits operating with up to 280 physical qubits. Using logical-level control and a zoned architecture in reconfigurable neutral-atom arrays7, our system combines high two-qubit gate fidelities8, arbitrary connectivity7,9, as well as fully programmable single-qubit rotations and mid-circuit readout10–15. Operating this logical processor with various types of encoding, we demonstrate improvement of a two-qubit logic gate by scaling surface-code6distance from d= 3 to d= 7, preparation of colour-code qubits with break-even fidelities5, fault-tolerant creation of logical Greenberger–Horne–Zeilinger (GHZ) states and feedforward entanglement teleportation, as well as operation of 40 colour-code qubits. Finally, using 3D [[8,3,2]] code blocks16,17, we realize computationally complex sampling circuits18with up to 48 logical qubits entangled with hypercube connectivity19with 228 logical two-qubit gates and 48 logical CCZ gates20. We find that this logical encoding substantially improves algorithmic performance with error detection, outperforming physical-qubit fidelities at both cross-entropy benchmarking and quantum simulations of fast scrambling21,22. These results herald the advent of early error-corrected quantum computation and chart a path towards large-scale logical processors.

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