Optimal control for Hamiltonian parameter estimation in non-commuting and bipartite quantum dynamics Abstract 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, especially in the presence of noise. Here, we extend optimally controlled estimation schemes for single qubits 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.