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Making use of coherence and entanglement as metrological quantum resources allows us to improve the measurement precision from the shot-noise or quantum limit to the Heisenberg limit. Quantum metrology then relies on the availability of quantum engineered systems that involve controllable quantum degrees of freedom which are sensitive to the measured quantity. Sensors operating in the qubit mode and exploiting their coherence in a phase-sensitive measurement have been shown to approach the Heisenberg scaling in precision. Here, we show that this result can be further improved by operating the quantum sensor in the qudit mode, i.e., by exploiting d rather than two levels. Specifically, we describe the metrological algorithm for using a superconducting transmon device operating in a qutrit mode as a magnetometer. The algorithm is based on the base-3 semiquantum Fourier transformation and enhances the quantum theoretical performance of the sensor by a factor of 2. Even more, the practical gain of our qutrit implementation is found in a reduction of the number of iteration steps of the quantum Fourier transformation by the factor ln(2)/ln(3)≈0.63 compared to the qubit mode. We show that a two-tone capacitively coupled radio-frequency signal is sufficient for implementation of the algorithm.