Gate-all-around integrated circuit structures having fin stack isolation, and methods of fabricating gate-all-around integrated circuit structures having fin stack isolation, are described. For example, an integrated circuit structure includes a sub-fin structure on a substrate, the sub-fin structure having a top and sidewalls. An isolation structure is on the top and along the sidewalls of the sub-fin structure. The isolation structure includes a first dielectric material surrounding regions of a second dielectric material. A vertical arrangement of horizontal nanowires is on a portion of the isolation structure on the top surface of the sub-fin structure.