We report for the very first time the controlled structural changes in the self-assemblies of N-(9-fluorenylmethoxycarbonyl)-O-tert-butyl-l-threonine (Fmoc-Thr(tBu)-OH) (FTU) to well defined unique morphologies. The self-assembling properties of FTU were very interesting and intriguing as it resulted in the formation of unusual structures which resembles fibrous dumbbells and double-sided broomstick-like morphologies along with conventional spheres and rods under controlled conditions of concentration and temperature. The self-assembly of other derivatives of threonine as well as another hydroxyl containing amino acid with same modification that is, ((N-(9H-fluoren-9-yl)methoxy)carbonyl)-O-(tert-butyl)-l-serine (Fmoc-Ser(tBu)-OH) (FSU) was also studied to understand the crucial role of –Fmoc, -tBu and an additional –CH3 group present in the structure of FTU in the process of self-assembly. Solvent dependent morphological studies of FTU and FSU suggest important role of solubility parameters and crystallization in formation of these unusual structures. The control experiments of co-incubation with tannic acid and urea and solution state 1H-NMR studies elucidate π–π stacking interactions as the key driving force for the structure formation. Further, the interactions which can occur between pairs of FTU and FSU which cause initial self-assembly was studied theoretically via computational modeling. These studies suggest pair of FTU can either interact via head-to-head (HH) or head-to-tail (HT) configurations and the most favorable probabilities of either of these interactions lead to morphological transitions in FTU self-assembly under varying conditions. The studies reported herein hence demonstrate that bioorganic molecules like protected single amino acids can be efficiently used as scaffold for self-assembly and provide a very simple and facile bottom-up-approach for the design of uncommon novel micro/nanoarchitects for multifarious applications. © 2023 Wiley Periodicals LLC.