Just as peptide function is determined by the position, sequence, and overall arrangement of constituent amino acids, the optical properties of nanoparticle (NP) assemblies are influenced by the size, dimensions, and arrangement of constituent NPs. In this work, we demonstrate that peptide sequence can be programmed to direct the structure and chiroptical activity of chiral helical gold NP (AuNP)superstructures, a growing class of chiral nanomaterials with potential in sensing, detection, and optics-based applications. Gold-binding peptide conjugate families, C-18-(PEPAuM,x)(2) and C-18-(PEPAuM-ox,x)(2), that differ in the position (x = 7, 9, and 11) of methionine (M)/methionine sulfoxide (M-ox) within the peptide sequences (PEPAu = AYSS-GAPPMPPF/PEPAuM-ox = AYSSGAPPM(ox)PPF) are employed to control the aspect ratio and size of AuNPs within helical NP assemblies. Computational modeling reveals that the amino acid variations have a profound effect on peptide-AuNP interactions that ultimately lead to control over NP size. C-18-(PEPAuM,x)(2) (x = 7, 9, and 11) yield irregular double-helical superstructures comprising spherical AuNPs, while C-18-(PEPAuM-ox,x)(2) (x = 9, 11) yield single-helical assemblies comprising oblong or rod-shaped AuNPs. Further, component AuNPs are larger when M/M-ox is placed at x = 11, while smaller component AuNPs are observed when M/M-ox is placed at x = 7. Changes in nanoscale structures manifest themselves in observable differences in chiroptical signal intensity. Ultimately, we achieve dramatic variance in the structure and properties of chiral AuNP superstructures via simple molecular-level tuning of peptide primary sequence.