In this work we address the challenge of furthering our understanding of the driving forces responsible for the metal–metal interactions in industrially relevant bimetallic nanocatalysts, by taking a comparative approach to the atomic scale characterization of two core–shell nanorod systems (AuPd and AuRh). Using aberration-corrected scanning transmission electron microscopy, we show the existence of a randomly mixed alloy layer some 4–5 atomic layers thick between completely bulk immiscible Au and Rh, which facilitates fully epitaxial overgrowth for the first few atomic layers. In marked contrast in AuPd nanorods, we find atomically sharp segregation resulting in a quasi-epitaxial, strained interface between bulk miscible metals. By comparing the two systems, including molecular dynamics simulations, we are able to gain insights into the factors that may have influenced their structure and chemical ordering, which cannot be explained by the key structural and energetic parameters of either system in isolation, thus demonstrating the advantage of taking a comparative approach to the characterization of complex binary systems. This work highlights the importance of achieving a fundamental understanding of reaction kinetics in realizing the atomically controlled synthesis of bimetallic nanocatalysts.