The reductive catalytic fractionation of flax shives in the presence of bimetallic NiRu catalysts supported on oxidized carbon materials (CM) such as mesoporous Sibunit and carbon mesostructured by KAIST (CMK-3) was studied. The catalysts based on CMK-3 were characterized by a higher surface area (1216 m2/g) compared to the ones based on Sibunit (315 m2/g). The catalyst supported on CMK-3 (10Ni3RuC400) was characterized by a more uniform distribution of Ni particles, in contrast to the Sibunit-based catalyst (10Ni3RuS450), on the surface of which large agglomerated particles (300–400 nm) were presented. The bimetallic catalysts were found to be more selective towards propanol-substituted methoxyphenols compared to monometallic Ru/C and Ni/C catalysts. A high yield of monomers (up to 26 wt%, including 17% 4-propanol guaiacol) was obtained in the presence of a 10Ni3RuC400 catalyst based on CMK-3.