The competition between the stability of the cubic and hexagonal full Heusler alloys and the implications concerning their magnetic properties were systematically studied through the detailed structural and magnetic characterization of the Fe2Mn(Si1−xGex) system. This system was specifically chosen as the parent compositions are cubic (x = 0) and hexagonal (x = 1). It is found that the formation of hexagonal phases occurs for the x ≥ 0.6 samples, whereas its phase fraction monotonically increases with x until the pure hexagonal Fe2MnGe is formed. The change in structure results in high sensitiveness of both the saturation of magnetization (MS) and Curie temperature (TC) with x values, related to a strong magnetocrystalline anisotropy of the hexagonal phase. Both cubic and hexagonal magnetic features were qualitatively reproduced by Density Functional Theory (DFT) calculations. This work provides an experimental and theoretical foundation for further design of Heusler systems with controlled structures and magnetic properties.