After detonation synthesis, primary nanodiamond particles are around 4–6 nm in size. However, they join into agglomerates with larger parameters and weak bonds between particles. The introduction of agglomerates into a metal matrix can lead to the weakness of composites. This paper demonstrates the possibility of obtaining a non-agglomerated distribution of nanodiamonds inside a metal matrix. The fabrication method was based on mechanical alloying to create additional stresses and deformations by phase transformations during treatment in a planetary mill. According to the findings, the starting temperature of the reaction between the non-agglomerated nanodiamonds and aluminium matrix reduces to 450 °C. Furthermore, the paper shows that existing methods (annealing for the transformation of a diamond structure into graphitic material and cleaning from this graphitic material) cannot reduce the sizes of nanodiamonds in the agglomerated state. Agglomerated nanodiamonds transform into carbon onions (graphitic material) during annealing in a vacuum in the following way: the nanodiamonds located in the surface layers of the agglomerate are the first to undergo the complete transformation followed by the transformation of nanoparticles in its deeper layers. In the intermediate state, the agglomerate has a graphitic surface layer and a core from nanodiamonds: cleaning from graphite cannot reduce nanodiamond particle size.