Polydopamine (PDA) is a nature inspired biopolymer that can be synthesized through self-assembly under mild controlled environment. Due to the catechol functional groups, PDA can form coordination bonding with various metallic ions. In our work, we utilized the strong affinity between PDA and various metal cations, including Cu2+, Ni2+, and Co2+, to obtain metal ion doped PDA (mPDA). The mPDA powders were irradiated under electron beam using a transmission electron microscope. As the electron beam intensity increased, nucleation and growth of nanoscale precipitates were observed. Electron diffraction and EDX analysis indicated these precipitations were metal nanocrystals. The morphology of the metal nanoparticles varied depending on the metal specie. This discovery indicates electron and perhaps other irradiation sources can be used to induce nanoparticle in metal-doped PDA, which may be useful to modify the properties of PDA-based thin film materials. On the other hand, our study implies PDA can be used as a platform for growth of nanoparticles, which may have potentials in various engineering applications.