The depletion of fossil resources is driving the research towards renewable alternatives, like lignocellulosic biomass. Therefore, the development of efficient continuous-flow processes, allowing to achieve better productivity compared to batch processes, will play a crucial role in promoting a sustainable transition. In this context, we report on the continuous-flow, gas-phase, catalytic transfer hydrogenation (CTH) of methyl levulinate and ethanol over zirconia catalysts, in particular focusing on the effect of two different crystalline phases (i.e. monoclinic, m-ZrO₂, and tetragonal, t-ZrO₂) on catalyst performance. An in-depth catalyst characterisation was coupled with both computational and ¹H-NMR relaxation studies to assess the structure-activity relationship, providing fundamental insights into the catalytic process and future catalyst optimization. The results, indicate that the higher Lewis acidity and basicity along with the lower affinity with ethanol of m-ZrO₂ with respect to t-ZrO₂ are responsible for the promotion of undesired oligomerisation reactions of angelica lactones responsible for catalyst deactivation.