Herein, an intricate interplay of the non-covalent interactions induced via subtle chemical modification around the flavin core was envisaged to generate a diverse array of morphological features. Three different flavin analogues with the covalently linked carboxylic group, a glycine or proline entity were chosen along with a simple flavin entity and were investigated for their photophysical and morphological behavior. A systematic structural variation around flavin core has resulted in the formation of irregular shaped, fibrous, tapered fibers, sphere shaped and punctured disc shaped self-assembled structures. Interestingly, the carboxylic-flavin analogue was found to differentiate between monovalent alkali versus divalent alkaline earth metal ions. Overall, the present study highlights the importance of subtle structural engineering in regulating the diverse modes for self-assembled structures, which might be playing a role in designing chemical structures for practical applications.