A quantum computing system and methods for performing fusion based quantum computing on encoded qubits. A fusion controller sequentially performs a series of fusion measurements on respective physical qubits of first and second encoded qubits to obtain a respective series of classical measurement results. For respective fusion measurements of the series of fusion measurements, a basis for performing the respective fusion measurement is selected based on classical measurement results of previous fusion measurements. An encoded fusion measurement result is determined based on the classical measurement results, and the encoded fusion measurement result is stored in a memory medium.