Ester, amide, and directly linked composites of squalene and cationic diaza [4]helicenes 1 are readily prepared. These lipid-dye constructs 2, 3, and 4 give in aqueous media monodispersed spherical nanoassemblies around 100–130 nm in diameter with excellent stability for several months. Racemic and enantiopure nanoassemblies of compound 2 are fully characterized, including by transmission electron microscope and cryogenic transmission electron microscope imaging that did not reveal higher order supramolecular structures. Investigations of their (chir)optical properties show red absorption maxima ≈600 nm and red fluorescence spanning up to the near-infrared region, with average Stokes shifts of 1350–1550 cm−1. Live-cell imaging by confocal microscopy reveals rapid internalization on the minute time scale and organelle-specific accumulation. Colocalization with MitoTracker in several cancer cell lines demonstrates a specific staining of mitochondria by the [4]helicene–squalene nanoassemblies. To our knowledge, it is the first report of a subcellular targeting by squalene-based nanoassemblies.