Combustion synthesis (CS) is a specific approach for fabrication of a variety of advanced materials through use of self-sustaining chemical reactions. Controlling over the microstructure of the material is a key factor in defining the maturity of a technology. In this work, we demonstrate that under specific conditions, morphology and microstructure of the initial reaction media do not change during the CS process. Thus, one may control the microstructure of CS materials by preparing the desired structure of the initial reaction media. Specifically, using examples from several systems, which include intermetallics (NiAl), ceramics (SiC) and refractory carbides (TiC), we demonstrate that combination of short-term high-energy ball milling and CS allows precise control over the morphology and phase composition of product powders.