Lipid lyotropic liquid crystalline nanoparticles (LCNPs) have attracted enormous attention for biomedical applications, such as drug delivery, due to their high biocompatibility and different structures giving rise to distinct properties. For e.g., tuning the nanostructure of LCNPs results in a significant difference in the release profile of encapsulated bioactives. However, it is uncertain whether these LCNPs retain their original structure upon contact with physiological relevant media at body temperature, and the link between their internal nanostructure and cell cytotoxicity. Here we will use SAXS to unravel the real-time phase behaviour of LCNPs with different cell media, and further investigate the relationship between nanostructure, cell cytotoxicity and uptake. The results will shed light on future strategies to transform LCNPs into a viable therapeutic entity ideal for biomedical applications.