A multi-scale mathematical model, which accounts for mass transport on the crystal and agglomerate length-scales, is used to investigate the electrochemical performance of lithium-magnetite electrochemical cells. Experimental discharge and voltage recovery data are compared to three sets of simulations, which incorporate crystal-only, agglomerate-only, or multi-scale transport effects. Mass transport diffusion coefficients are determined by fitting the simulated voltage recovery times to experimental data. In addition, a further extension of the multi-scale model is proposed which accounts for the impact of agglomerate size distributions on electrochemical performance. The results of the study indicate that, depending on the crystal size, the low utilization of the active material is caused by transport limitations on the agglomerate and/or crystal length-scales. For electrodes composed of small crystals (6 and 8 nm diameters), it is concluded that the transport limitations in the agglomerate are primarily responsible for the long voltage recovery times and low utilization of the active mass. In the electrodes composed of large crystals (32 nm diameter), the slow voltage recovery is attributed to transport limitations on both the agglomerate and crystal length-scales.