AbstractQuantum information processing promises to revolutionise computing; quantum algorithms have been discovered that address common tasks significantly more efficiently than their classical counterparts. For a physical system to be a viable quantum computer it must be possible to initialise its quantum state, to realise a set of universal quantum logic gates, including at least one multi-qubit gate, and to make measurements of qubit states. Molecular Electron Spin Qubits (MESQs) have been proposed to fulfil these criteria, as their bottom-up synthesis should facilitate tuning properties as desired and the reproducible production of multi-MESQ structures. Here we explore how to perform a two-qubit entangling gate on a multi-MESQ system, and how to readout the state via quantum state tomography. We propose methods of accomplishing both procedures using multifrequency pulse Electron Paramagnetic Resonance (EPR) and apply them to a model MESQ structure consisting of two nitroxide spin centres. Our results confirm the methodological principles and shed light on the experimental hurdles which must be overcome to realise a demonstration of controlled entanglement on this system.