In the present manuscript, the luminescence and the self-assembly behaviour of two aromatic dipeptides with a singular structure variable are investigated. The terminally protected dipeptides tryptophan–tyrosine (WYp) and tryptophan–phenylalanine (WFp) were synthesized using a standard solution phase procedure. Significant solvatochromic effect was observed for both the dipeptidyl entities; whilst the influence was more pronounced for the WYp entity when compared with WFp. Interesting morphological variation was observed for WFp and WYp, in which discrete and interconnected nanospheres were observed for the respective dipeptides. The results obtained signify the influence of the singular structural variation on modulating the overall functional behaviour of the short peptides motifs. © 2022 John Wiley & Sons Ltd.