Addressing and mitigating decoherence sources plays an essential role in the development of a scalable quantum computing system, which requires low gate errors to be consistently maintained throughout the circuit execution. While nuclear spin-free materials, such as isotopically purified silicon, exhibit intrinsically promising coherence properties for electron spin qubits, the omnipresent charge noise, when converted to magnetic noise under a strong magnetic field gradient, often hinders stable qubit operation within a time frame comparable to the data acquisition time. Here, we demonstrate both open- and closed-loop suppression techniques for the transduced noise in silicon spin qubits, resulting in a more than two-fold (ten-fold) improvement of the inhomogeneous coherence time (Rabi oscillation quality) that leads to a single-qubit gate fidelity of over 99.6% even in the presence of a strong decoherence field gradient. Utilizing gate set tomography, we show that adaptive qubit control also reduces the non-Markovian noise in the system, which validates the stability of the gate fidelity. The technique can be used to learn multiple Hamiltonian parameters and is useful for the intermittent calibration of the circuit parameters with affordable experimental overhead, providing a useful subroutine during the repeated execution of general quantum circuits.