Heterogeneous catalytic hydrotreatment is recognized as a key valorization route of bio-based oxygenates in a bio-refinery concept. Catalytic hydrodeoxygenation (HDO) and hydrogenation of eugenol, a lignin building block model component, was investigated in silico and experimentally in a three-phase slurry reactor over the ruthenium supported on carbon (Ru/C) and by using hexadecane (HD) solvent. The influence of operating process conditions on the activity and selectivity of the transformations was determined; specifically, the temperature (225-325 °C), hydrogen gas pressure (4-7 MPa), catalyst loading (0-0.35 wt%), eugenol loading (0-5 wt%), process gas (H2 and N2), stirring speed (100-1000 min-1) were varied within the listed values. Based on the detailed chromatographic, spectroscopic, microscopic, temperature-programed desorption, reduction, oxidation or physisorption analysis of solid, liquid and gas phase, a rather complex reaction-pathway network for eugenol hydrotreatment was proposed. Experimental results revealed that allyl group and benzene ring saturation was favored in comparison to competitive deoxygenation reactions, namely dehydroxylation and demethoxylation of oxygen moieties on aromatic ring. The mechanism of ketone group formation has been clarified among various proposed pathways in the literature, as it most likely proceeds via keto-enol isomerization. Precursors responsible for cyclohexane-ring contraction to substituted 5-member ring compounds were also identified and mechanism and kinetics of transformation was proposed. Intrinsic microkinetic modelling was based on the proposed network of parallel and consecutive homogeneous and catalytic reactions, and accounted the gas–liquid and liquid–solid mass transfer, adsorption and desorption kinetics and thermodynamic equilibria. Model results indicate 36- and 42-times higher demethoxylation and dehydroxylation rate constants for aromatics in comparison to corresponding oxygen-containing cycloalkanes.