Electronic-structure methods based on density-functional theory (DFT) were used to directly quantify the effect of chemical short-range order (SRO) on thermodynamic, structural, and electronic properties of archetypal face-centered-cubic (fcc) Cu3Au alloy. We show that SRO can be tuned to alter bonding and lattice dynamics (i.e., phonons) and detail how these properties are changed with SRO. Thermodynamically favorable SRO improves phase stability of Cu3Au from − 0.0343 eV-atom−1 to −0.0682 eV-atom−1. We use DFT-based linear-response theory to predict SRO and its electronic origin, and accurately estimate the transition temperature, ordering instability (L12), and Warren-Cowley SRO parameters, observed in experiments. The accurate prediction of real-space SRO gives an edge over computationally and resource intensive approches such as Monte-Carlo methods or experiments, which will enable large-scale molecular dynamic simulations by providing supercells with optimized SRO. We also analyze phonon dispersion and estimate the vibrational entropy changes in Cu3Au (from 9kB at 300–6kB at 100 K). We establish from SRO analysis that exclusion of chemical interactions may lead to a skewed view of true properties in chemically complex alloys. The first-principles methods described here are applicable to any arbitrary complex solid-solution alloys, including multi-principal-element alloys, so hold promise for designing technologically useful materials.