Among the plethora of aromatic and aliphatic dipeptide sequences that are successfully employed in nanoarchitecture and nanotechnology, dileucines (Leu‐Leu) is known for its self‐sorting behavior like diphenylalanine (Phe‐Phe), the most explored motif till date. However, only a few reports demonstrate the effects of capping groups on Leu‐Leu self‐assembly. Hence, to understand the effect of hydrophobic substituent on C‐/N‐termini, a series of Leu‐Leu derivatives are prepared and their self‐assembled morphology is evaluated. Spherical and tubular mesoscopic morphologies of C‐ and N‐termini capped Leu‐Leu owing to H‐bonding, π‐π stacking and van der Waals interactions are reported. Attachment of alkynes (propyne) at C‐termini results in micro‐tubes and rods for Boc‐Leu‐Leu‐Propyne and Fc‐Leu‐Leu‐Propyne, respectively. Hollow morphology was observed and substantiated by TEM and confocal microscopy. These micro‐tubes and micro‐rods transform into spherical nanoparticles after click conjugation at C‐termini which clearly show the effect of chemical modification on their self‐assembly. Therefore, subtle variations of capping groups result in remarkable changes of self‐assembled morphology, which suggests that the terminal capping is an important factor for rational design of short peptide‐based biomaterial.