Well-dispersed Pd nanoparticles have been synthesized inside the mesoporosity of a silica monolith featuring hierarchical porosity of homogeneous interconnected macropores (4 microns) and mesopores (11 nm). These monoliths have been implemented as microreactors for selective hydrogenation reactions. Conversion and selectivity can be tuned by adjusting the flow rates of hydrogen and substrates. In the selective hydrogenation of cyclooctadiene, a conversion of 95% and a selectivity of 90% in the monohydrogenated product, constant over a period of 70 h, have been reached. These figures correspond to a productivity of 4.2 mmol s−1 g−1MonoSil (or 0.32 mol s−1 g−1Pd). In the stereoselective hydrogenation of 3-hexyn-1-ol a constant conversion of 85% was observed, with however moderate selectivity into the cis isomer, over a test period of 7 h. These results open the route to the synthesis of important chemicals and intermediates via safe and green processes.