In the last two decades, extracellular vesicles (EVs) from the three domains of life, archae, bacteria and eukaryota, have gained increasing scientific attention. As such, the role of EVs in host-pathogen communication and immune modulation are being intensely investigated. Pivotal to EV research is the determination of how and where EVs are taken up by recipient cells and organs in vivo, which requires suitable tracking strategies including labelling. Labelling of EVs is often performed post-isolation which increases risks of non-specific labelling and the introduction of labelling artefacts. Here we exploited the inability of helminths to de novo synthesise fatty acids to enable labelling of EVs by whole organism uptake of fluorescent lipid analogues and the subsequent incorporation in EVs. We showed uptake of DOPE-Rhodamine in Anisakis spp. and Trichuris suis larvae. EVs isolated from supernatant of Anisakis spp. labelled with DOPE-Rhodamine were characterised to assess effects of labelling on size, structure and fluorescence of EVs. Fluorescent EVs were successfully taken up by the human macrophage cell line THP-1. This study therefore presents a novel staining method that can be utilized by the EV field in parasitology and potentially across multiple species.