A series of phenalenone-lipid conjugates (1A, 1B, 1C, 2) have been synthesized to compensate for the poor water solubility of the photosensitizer phenalenone (PN) and promote the formation of nano-assemblies. We show that the organization and structure of monolayers upon compression strongly depend on the nature of the linker connecting PN to the lipid backbone, and the number of C18 chains. Monolayer properties at the air-water interface were analyzed by surface pressure measurements, Brewster angle and atomic force microscopies, grazing incidence X-ray diffraction, and X-ray reflectivity. Whereas conjugate 1C (ester bond) organizes into multilayers upon compression, conjugates 1A, 1B, and 2 form stable monolayers whose structure is controlled by van der Waals (vdW) interactions between C18 chains, intermolecular H-bonding involving the linker, and for 1B, π-π stacking of PN moieties. Conjugate 1A (amide-triazole linker) is structured into a rectangular network of chains with an order that extends only to the molecule of the adjacent cell. Conjugate 1B (amide bond) forms two incommensurate networks, one for the chains and the other for the headgroups. The distance between molecules in the next near neighbor chain lattice and the sufficient degree of freedom of PN groups allows them to pile up via π-π interactions below the chains in a rectangular cell. Conjugate 2 with its double chain adopts a similar behavior to that of a saturated phospholipid. Strong vdW interactions predominate and allow, at high surface pressure, hexagonal packing with no chain tilt. The distance between molecules prevents PN stacking. The identified PN derivative structures explain the linker’s impact on the formation and stability of nano-assemblies.