Dynamic proteoids are dynamic covalent analogues of proteins which are generated through the reversible polymerization of amino-acid- or peptide-derived monomers. The authors design and prepare a series of dynamic proteoids based on the reversible polycondensation of six types of dipeptide hydrazides bearing different categories of side chains. The polymerization and structures of biodynamers generated by 1 H-NMR spectroscopy, light scattering and cryo-transmission-electron microscopy are studied. This study shows that the presence of aromatic rings in the side chains plays the most essential role in determining the extent of the polymerization and organization into resultant nanostructures through π-π-stacking interactions, hydroxyl groups have a less favorable influence via hydrogen bonds, whereas a high density of positive charge blocks the generation of biodynamers due to electrostatic repulsions. These findings set the stage for the rational design and synthesis of dynamic proteoids as novel biofunctional materials.