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We describe a combined electrochemical and first principle density functional study to probe the corrosion inhibiting and adsorption behavior of methionine (Met) and phenylalanine (Phe) on polycrystalline and nanocrystalline iron in acid media. Met functioned as a better inhibitor for both Fe microstructures, and was more favorably adsorbed on the nanocrystalline surface. The nanocrystalline surface however diminished adsorption of Phe. The comparable values of our computed physisorption energies (-94.2 kcal mol(-1) and -86.6 kcal mol(-1) for Phe and Met respectively) as well as the stable adsorption orientations of both molecules on Fe suggest a controlling influence of a soft epitaxial adsorption mechanism in which C, N, O, S atoms of the molecules align with epitaxial grooves on the Fe lattice. The significant contribution of physisorptive interactions also correlates with the similarity in experimental inhibition efficiencies on polycrystalline Fe (Phe = 73% and Met = 82%), though for Met the thiol group imparts an added ability for covalent interaction with Fe, which accounts for the higher efficiency. Furthermore, we have related the diminished inhibition efficiency of Phe on the nanocrystalline Fe surface to disruption of the epitaxial patterns on the lattice as the surface becomes increasingly defective, leading to weaker adsorption. The improved efficiency of Met on the nanocrystalline surface is related to scaling up of the covalent interactions around defect sites. Our theoretical conclusions are validated by the consistency with our experimental findings.