Subcellular compartmentation is a hallmark of all eukaryotic cells and in the past has mostly been discussed in terms of a separation of different metabolic pathways. However, in the cellular context these different activities need to be coordinated and adjusted to changing environmental conditions involving a great variety of different signalling mechanisms and pathways. While some of them have been known for many years, a number of completely novel pathways and signalling mechanisms have been discovered only recently. They involve a surprisingly broad range of metabolites, secondary messengers and hormones, as well as proteins such as transcription factors and protein kinases. At the time of the last Journal of Experimental Botany special issue on organellar signalling in 2012 (e.g. see Teige, 2012) there was a focus on identification of novel components and description of general mechanisms. Much progress has been achieved since then, particularly in the latter area, and therefore here we emphasize emerging novel connections between different signalling pathways and the specific mechanisms involved.