This paper presents the study of the dynamics of the formation of polymer-assisted highly-orientated polycrystalline cubic structures (CS) by a fractal-mediated mechanism. This mechanism involves the formation of seed Ag@Co nanoparticles by InterMatrix Synthesis and subsequent overgrowth after incubation at a low temperature in chloride and phosphate solutions. These ions promote the dissolution and recrystallization in an ordered configuration of pre-synthetized nanoparticles initially embedded in negatively-charged polymeric matrices. During recrystallization, silver ions aggregate in AgCl@Co fractal-like structures, then evolve into regular polycrystalline solid nanostructures (e.g. CS) in a single crystallization step on specific regions of the ion exchange resin (IER) which maintain the integrity of polycrystalline nanocubes. Here, we study the essential role of the IER in the formation of these CS for the maintenance of their integrity and stability. Thus, this synthesis protocol may be easily expanded to the composition of other nanoparticles providing an interesting, cheap and simple alternative for cubic structure formation and isolation.