Carbon deposition during CO methanation from biomass-derived gas is a significant challenge in terms of catalyst lifetime. It results from the severe reaction conditions imposed by the presence of unsaturated hydrocarbons in the gasified feedstock. This work investigated the structure of boron-modified Ni/Al2O3 catalysts exhibiting enhanced carbon resistance. As a consequence of B promoting the growth of Ni crystallites, the structure of the B-modified catalyst was demonstrated to be different at the nanoscale, especially after calcination. The modified catalyst possesses larger Ni particles with porous regions in which B is present. The absence of carbidic and amorphous carbon species, which are considered critical for catalyst deactivation in low-temperature processes, confirms that B effectively prevents carbon diffusion into Ni, which thus enhances the durability of the catalyst for CO methanation. These results may reveal a strategy of wider significance for developing catalysts with improved stability.