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In this work, we show how to obtain internal monodispersed gold nanoparticles inside polydopamine (PDA) nanospheres that are also externally decorated with gold. The number of internal nanoparticles is affected by the size of the PDA nanosphere used, and the lower limit in the number of gold nanoparticles in the center of decorated nanospheres, one single gold nanoparticle, has been reached. In addition, extensive molecular dynamics simulations of PDA nanospheres based on four different chemical motifs, in the presence of water and with different sizes, have been performed to gain insight into the arrangements capable of accommodating cavities. In particular, PDA nanospheres based on pyranoacridinotrione (PYR) units provide good agreement with the experimental attainment of internal metal nanoparticles. In these, the stacking of PYR units leads to a particular morphology, with large portions of space occupied by the solvent, that would explain the observed formation of gold nanoparticles inside the PDA nanosphere.