The reaction evolution and kinetics of the LiFePO4 positive electrode material is dependent on the synthesis method and cycling conditions. In operando neutron powder diffraction is used investigate the structure-electrochemistry relationship of the electrode materials in a Valence Technology Inc. 18650 Energy cell (IFR18650EC) containing a graphite negative electrode and a Mg-doped LiFePO4 (Li(MgFe)PO4) positive electrode. Two cells were studied at ambient (298 K) and elevated (323 K) temperature, and higher temperatures were found to improve reaction kinetics and hence capacity. Rietveld refinement of structural models against the diffraction data revealed information about the nucleation of the lithiated and delithiated phases in the Li(MgFe)PO4 positive electrode material as a function of each cell's state of charge. Polarisation was indicated by a shift in the potential at which the lithiated and delithiated (MgFe)PO4 phases nucleate during cycling, the extent of which was found to be linearly proportional to the applied current. This work provides new evidence for polarisation of the positive electrode material in a Li-ion battery system.