The processes of palladium deposition on various high-porosity carbon matrices (Sibunit, CMK-3) have been studied. Mesostructured carbon material CMK-3 was synthesized using a silicate template of SBA-15 type. Pd nanoparticles were loaded onto carbon matrices by metalorganic chemical vapour deposition (MOCVD) method using palladium(II) acetylacetonate precursor. Bimetal Au–Pd systems were synthesized by autoclave reduction of gold(III) chloride complexes on Pd-containing carbon matrices. Structure of the obtained composite particles was studied by electron microscopy and X-ray diffraction. The average diameter of Pd particles on Sibunit is about 10, and 5–6 nm on CMK-3. The catalytic activity of the synthesized materials was studied in the reaction of furfural diethyl acetal (FDEA) hydrogenation, using gas–liquid chromatographic analysis. There is significant difference in catalytic activity of MOCVD-Pd/C compared to conventional impregnated Pd/C systems: the hydrogenation rate is 3–6 times higher with MOCVD-derived catalysts. Introducing Au into a MOCVD-Pd/C catalyst increases the hydrogenation rate threefold. Considerable difference in the composition of hydrogenation products was observed between these differently prepared catalysts.