Methods, systems, and apparatus for parallel optimization of continuously running quantum error correction by closed-loop feedback. In one aspect, a method includes continuously and effectively optimizing qubit performance in-situ whilst an error correction operation on the quantum system is miming. The method directly monitors the output from error detection and provides this information as feedback to calibrate the quantum gates associated with the quantum system. In some implementations, the physical qubits are spatially partitioned into one or more independent hardware patterns, where the errors attributable to each hardware pattern are non-overlapping. The one or more different sets of hardware patterns are then temporarily interleaved such that all physical qubits and operations are optimized. The method allows for the optimization of each section of a hardware pattern to be performed individually and in parallel, and can result is O(1) scaling.