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Classical deformation mechanisms based on crystalline defects of metallic polycrystals are not entirely suitable to describe the mechanical behavior of nanocrystalline and glassy materials. Their inherent complexity creates a real challenge to understand the acting physical phenomena. Thus, the molecular dynamics approach becomes interesting because it allows evaluating the mechanical properties and its related atomic structure. To study the atomic structure's influence on the deformation mechanisms at the nanoscale level of the Al80Ti15Ni5 alloy, molecular dynamics simulations, and post-processing techniques were used in the present work. The results revealed a significant dependency between the Young modulus and the atomic structure. Moreover, the type of structure, i.e., nanocrystalline or amorphous, governs the deformation mechanism type. For the nanocrystalline alloy, grain boundary sliding and diffusion seem to be the dominant deformation processes followed by the less essential emissions of partial dislocations from the grain boundaries. Concerning the amorphous material, the shear transformation zones begin to form in the elastic regime evolving to shear bands, these being the main mechanisms involved in the deformation process. The results also indicate the amorphous structure as a lower limit-case of the nanocrystal. The Al80Ti15Ni5 elastic moduli values were below expectations; for this reason, the effects of unary and ternary interatomic potentials were evaluated for each element.