In order to convert overfunctionalized biomass-derived compounds into chemicals and fuels a catalyst is needed to effect hydrodeoxygenation (HDO), i.e., the combination of iterative acid-catalyzed dehydration and metal catalyzed hydrogenations/hydrogenolysis to decrease the content of oxygen. To meet this goal, the complexes [(4'-Ph-terpy)Ir(OTf)3] (4'-Ph-terpy = 4'-phenyl-2,2':6'6"-terpyridine) and [Ru(triphos)(CH3CN)3](OTf)2 (triphos = 1,1,1-tris(diphenylphosphinomethyl) ethane) were prepared and evaluated as water-, acid- and high-temperature stable homogeneous catalysts for the hydrogenation of biomass-derived 2,5-hexanedione and 2,5-dimethylfuran (2,5-DMF) to value added chemicals. At T ≥ 175 °C the iridium system decomposed to a combination of a highly active heterogeneous Ir0 on the reactor walls and an inactive [M(4'-Ph-terpy)2]n+ compound (M = Fe, Ni, Ru, Ir; n = 2, 3) characterized by ESI-MS and single crystal X-ray crystallography, in which the source of the Fe and Ni was metal leaching from the 316SS reactor body. [Ru(triphos)(CH3CN)3](OTf)2 on the other hand was an effective homogeneous catalyst for the hydrogenation of 2,5-hexanedione and 2,5-DMF at temperatures between 150 and 200 °C. This catalyst became deactivated by formation of the bridging compound [Ru2(μ-OH)3(triphos)2](OTf), but could be reactivated by the addition of an acid co-catalyst. The hydrogenation of 2,5-hexanedione showed a first order rate dependence on hydrogen pressure as determined by direct hydrogen uptake rate measurements. With furfuryl alcohol — a more challenging substrate — only marginal conversions to hydrogenated products were observed. In an attempt to improve the catalyst activity by improving the water solubility, [Ru(NCCH3)3(N-triphos)](CF3SO3)2 was prepared and was able to convert furfuryl alcohol to 1,4-pentanediol in modest yield (26%), but still exhibited lower than desired water solubility under either neutral or acidic conditions at room temperature.