During cellular trafficking, the Golgi and the trans-Golgi network (TGN) are key for processing, sorting and packaging of cargo proteins to ensure arrival at their final destination. Whereas the Golgi comprises flat membranes or cisternae, the TGN is composed of tubular-reticular membranes and located at the trans-Golgi side. Now, Takuro Tojima and co-workers (Tojima et al., 2019) set out to dissect the spatiotemporal transition dynamics from Golgi to TGN using their previously developed super-resolution confocal live imaging microscopy (SCLIM) technique. The authors create numerous fluorescent fusion proteins for Golgi- and TGN-resident proteins and perform colocalisation mapping of these proteins in the cisternae and TGN of budding yeast. As a result, they define the Golgi–TGN transition as three stages: the Golgi stage, characterised by glycosylation; an early TGN stage, during which cargos from the retrograde traffic are received; and the late TGN stage, when transport carrier formation occurs. Interestingly, the authors observe compartmentalisation of early and late stage proteins within the same cisterna, for example for t-SNARE and clathrin. In summary, this work provides evidence for a functional and structural compartment separation of the Golgi and the TGN in yeast.