Second Harmonic Scattering (SHS) is a suitable technique to investigate the orientational correlations between molecules. This article explores the organization of different dye molecules adsorbed within the hydrophobic porosity of a hybrid organic–inorganic nanotube. Experimental polarization resolved SHS measurements highlight different orientational orders ranking from highly ordered and rigid organizations to disordered assemblies. Microscopic models of assemblies inside the pores are presented and discussed in the context of orientational correlation between the dye molecules. This work shows that the degree of order in the nanotube cavity follows the molecule’s affinity within the porosity.