Optimisation of a heterogeneous catalytic process requires characterisation of the catalyst at industrially-relevant conditions and lengthscales. Here we use magnetic resonance imaging to gain insight into Fischer-Tropsch synthesis occurring in a pilot-scale fixed-bed reactor operating at 220 °C, 37 bar, and for three H2/CO feed ratios. Molecular diffusion and carbon number of hydrocarbon products are spatially-resolved within both the reactor and individual 1 wt% Ru/TiO2 catalyst pellets. These data highlight the importance of mass transfer, in addition to nanoscale catalyst activity, on catalyst performance. In particular, a start-up time of up to 3 weeks is required for steady-state to be achieved in the catalyst pores. Further, the average carbon number present in the pores can be as much as double that in the product wax.