Construction of complex three-dimensional (3D) architectures through hierarchical self-assembly of peptide molecules has become an attractive approach of fabricating multifunctional advanced materials due to their various potential applications in bionanotechnology. This paper describes the tunable formation of flower-like 3D hierarchical architectures of intricate morphology from a simple self-assembling dipeptide phenylalanine-tyrosine with a facile preparative method by applying a range of voltages through a drop of peptide solution. The fine-tuning of voltages and their application time enable to produce morphological changes of the microstructures from 2D to 3D and also control their formation. The morphology has been characterized by the gradual change in the height-to-diameter ratio of the microstructures with change in the applied voltages. Moreover, these microstructures show significant thermal stability over a wide range of temperatures, whereas adequately high temperature promotes the morphological transformation of the microstructures into different types of ultrathin 1D nanostructures such as nanowires, nanofibrils, etc. Furthermore, we have suggested a possible growth model for the fabrication of unique hierarchical architectures through diffusion-limited aggregation mechanism.