The Golgi apparatus is a highly organized and dynamic organelle that receives and distributes material from and to the endoplasmic reticulum (ER) and the endocytic pathway. One open question about Golgi organization is whether it is solely based on ER-to-Golgi transport. Here, we analyzed the kinetics of Golgi breakdown in the absence of COPII-dependent ER export with high temporal and spatial resolution using quantitative fluorescence microscopy. We found that Golgi breakdown occurred in two phases. While Golgi enzymes continuously redistributed to the ER, we consistently observed extensive Golgi fragmentation at the beginning of the breakdown, followed by microtubule-dependent formation of a Golgi remnant structure (phase1). Further Golgi disintegration occurred less uniformly (phase2). Remarkably, cisternal Golgi morphology was lost early in phase1 and Golgi fragments were instead corresponding to variably-sized vesicle clusters. These breakdown intermediates were devoid of COPI-dependent recycling material, but contained typical “core” Golgi components. Furthermore, Golgi breakdown intermediates were able to disassemble and reassemble following cell division, indicating that they retained important regulatory capabilities. Together, these findings support the view that Golgi self-organization exists independent of ER-to-Golgi transport.