Updated project metadata. The model pennate diatom Phaeodactylum tricornutum is able to assimilate a range of iron sources. It therefore provides a platform to study different mechanisms of iron processing concomitantly in the same cell. In this study we follow the localisation of three iron starvation induced proteins (ISIPs) in vivo, driven by their native promoters and tagged by fluorophores in an engineered line of P. tricornutum. In a proteomic analysis, we identify that the cell engages the endocytosis machinery involved in the vesicular trafficking as a response to siderophore molecules, even when these are not bound to iron. We find that the localisation patterns of ISIPs are dynamic and variable depending on the overall iron status of the cell and the source of iron it is exposed to. Notwithstanding, a common destination of the proteins is a globular compartment in the vicinity of the chloroplast, consistent with our proteomic findings, which point to the engagement of the cell’s vesicular network. We propose that this may be a dedicated iron processing site inside the periplastidial compartment of diatoms.