This work presents an advanced reactor selection strategy that combines elements of a knowledge-based expert system to reduce the number of feasible reactor configurations with elaborated and automatised process simulations to identify reactor performance parameters. Special focus was given to identify optimal catalyst loadings and favourable conditions for each configuration to enable a fair comparison. The workflow was exemplarily illustrated for the Ru/C-catalysed hydrogenation of arabinose and galactose to the corresponding sugar alcohols. The simulations were performed by using pseudo-2D reactor models implemented in Aspen Custom Modeler® and automatised by using the MS-Excel interface and VBA. The minichannel packings, namely wallcoated minichannel reactor (MCWR), minichannel reactor packed with catalytic particles (MCPR), and minichannel reactor packed with a catalytic open-celled foam (MCFR), outperform the conventional and miniaturised trickle-bed reactors (TBR and MTBR) in terms of space-time yield and catalyst use. However, longer reactor lengths are required to achieve 99% conversion of the sugars in MCWR and MCPR. Considering further technical challenges such as liquid distribution, packing the reactor, as well as the robustness and manufacture of catalysts in a biorefinery environment, miniaturised trickle beds are the most favourable design for a production scenario of 5000 t/a galactitol. However, the minichannel configurations will be more advantageous for reaction systems involving consecutive and parallel reactions and highly exothermic systems.