We report the formation of new phases in bimetallic Au-Cu nanoparticles. These phases were observed in nanoparticle synthesised by adopting a three-step protocol in a single pot. Nanoparticles at 180°C for 1 h led to the formation of single-phase solid solution of Cu in Au. Subsequent heat treatment at 290°C for 2 h of these Au-Cu nanoparticles revealed three new phases. One of them relates to the modification of occupancy of Cu in an ordered AuCu tetragonal phase (tP4). This cell although retains tetragonal symmetry but displays metrical properties akin to that of a cube. The other two relates to vacancy ordering along directions in the {111} planes of an ordered AuCu3 cubic phase (cP4). On the one hand, statistical occupancy of vacancy on Cu site in this cell leads to the reduction of cell size from ∼3.75 Å to ∼3.5 Å whereas ordering of vacant layer on the other hand gives rise to symmetry breaking. Former continues to display cubic symmetry whereas latter transforms to a trigonal cell.