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A novel reactor based on a bubble column staged by structured catalytic layers with integrated cross flow micro-heat-exchangers (HEX) was designed and tested in the solvent free hydrogenation of 2-methyl-3-butyn-2-ol (MBY) aiming on process intensification. The heat transfer performance of the HEX was determined for both single- and two-phase flow. The reaction side heat transfer coefficient was found to decrease considerably when gas was added to the feed stream. Similar to single-phase conditions, the heat transfer coefficient increased linearly with gas and liquid superficial velocity, u0,G and u0,L. Change from water to organic media decreased heat transfer in HEX element and the influence of u0,G and u0,L diminished. The HEX integrated within a staged bubble column reactor (SBCR) with catalytic layers made of Pd/ZnO on sintered metal fibers showed a high specific productivity in the solvent free hydrogenation of MBY. Despite the observed influence of external mass transfer on the overall catalyst performance, the SBCR productivity was several orders of magnitude above the values obtainable in conventional multiphase reactors.