We show that supported Ni, Pt, and Pd catalysts used for liquid phase hydrogenation are inhibited by the biogenic impurities present in biologically-derived feedstocks used to produce high-value chemicals. The effects of thiamine HCl, cysteine, methionine, biotin, tryptophan, niacin, threonine, and p-aminobenzoic acid were elucidated by collecting adsorption isotherms of these species and by quantifying their influence on the rate of cyclohexene hydrogenation at 323 K. Inhibition increases in the order of Pd \ Pt \ Ni and generally correlates with the binding energies of sulfur and nitrogen. The equilibrium constants reported here for adsorption of these species on Ni, Pt, and Pd can facilitate the design of separation systems and new catalysts used for upgrading biologically-produced platform molecules.