Cyclo(Gly-L-Lys) ε-amino derivatives (1 and 2) were synthesised and exploited as low molecular weight (LMW) gelators and ordered hierarchical structures. Cyclic dipeptide (CDP) derivative 1 forms organogels in hexane, carbon tetrachloride, toluene and chloroform at minimal gelation concentrations (MGC) 5.5 wt%, 4.4 wt%, 2.6 wt% and 3.2 wt% respectively. Organogel (toluene) and hydrogel were obtained using CDP 2 at a MGC of 3.2 wt% and 2.5 wt% respectively. Interestingly, CDP 2 exhibits excimer emission in chloroform and self-assembles into ordered microporous hierarchical structures. The insight into supramolecular self-assembly of CDPs into nanofibres and ordered hierarchical structures was achieved by microscopy analysis. Presence of a network of strong intermolecular hydrogen bonding and aromatic π–π interactions was validated through concentration and temperature dependent NMR studies.