The adsorption of three homo-tri-peptides, HHH, YYY and SSS, at the aqueous Au interface is investigated, using molecular dynamics simulations.We find that consideration of surface facet effects, relevant to experimental conditions, opens up new questions regarding interpretations of current experimental findings. Our well-tempered metadynamics simulations predict the rank ordering of the tri-peptide binding affinities at aqueous Au (111) In a separate set of simulations, we predict the structures of the adsorbed tri-peptides at the two aqueous Au facets, revealing facet-dependent differences in the adsorbed conformations. Our findings suggest that Au facet effects, where relevant, may influence the adsorption structures and energetics of biomolecules, highlighting the possible influence of the structural model used to interpret experimental binding data.