Inclusion complex formation between lipophilic dye molecules and amylose polymers in starch granules is investigated using laser spectroscopy and microscopy. By combining confocal laser scanning microscopy (CLSM) with spatial resolved photoluminescence (PL) spectroscopy, we are able to discriminate the presence of amylose in the peripheral region of regular and waxy granules from potato and corn starch, associating a clear optical fingerprint with the interaction between starch granules and lipophilic dye molecules. We show in particular that in the case of regular starch the polar head of the lipophilic dye molecules remains outside the amylose helix experiencing a water-based environment. The measurements performed on samples that have been extensively washed provide a strong proof of the specific interaction between lipid dye molecules and amylose chains in regular starch. These measurements also confirm the tendency of longer amylopectin chains, located in the hilum of waxy starch granules, to form inclusion complexes with ligands. Through real-time recording of CLSM micrographs, within a time frame of tens of seconds, we measured the dynamics of occurrence of the inclusion process between lipids and amylose located at the periphery of starch granules.