Here we use fluorescence lifetime imaging microscopy (FLIM) to study the supramolecular organization of nanoencapsulated liposomal all-trans retinoic acid (ATRA), exploiting ATRA's intrinsic fluorescence as a source of signal and phasor transformation as a fit-free analytical approach to lifetime data. Our non-invasive method is suitable for checking for the presence of a fraction of ATRA molecules interacting with liposomal membranes. The results are validated by independent small-angle X-ray scattering (SAXS) and nano-differential scanning calorimetry (NanoDSC) measurements, probing ATRA's putative position on the membrane and effect on membrane organization. Besides the insights on the specific case-study proposed, the present results confirm the effectiveness of Phasor-FLIM analysis in elucidating the nanoscale supramolecular organization of fluorescent drugs in pharmaceutical formulations. This underscores the importance of leveraging advanced imaging techniques to deepen our understanding and optimize drugs' performance in delivery applications.