The ability to characterise a Hamiltonian with high precision is crucial for the implementation of quantum technologies. In addition to the well-developed approaches utilising optimal probe states and optimal measurements, the method of optimal control can be used to identify time-dependent pulses applied to the system to achieve higher precision in the estimation of Hamiltonian parameters, especially in the presence of noise. Here, we extend optimally controlled estimation schemes for single

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... bits to non-commuting dynamics as well as two interacting qubits, demonstrating improvements in terms of maximal precision, time-stability, as well as robustness over uncontrolled protocols.