Three-layer iron-rich Fe3+xSi1−x/Ge/Fe3+xSi1−x (0.2 < x < 0.64) heterostructures on a Si(111) surface with Ge thicknesses of 4 nm and 7 nm were grown by molecular beam epitaxy. Systematic studies of the structural and morphological properties of the synthesized samples have shown that an increase in the Ge thickness causes a prolonged atomic diffusion through the interfaces, which significantly increases the lattice misfits in the Ge/Fe3+xSi1−x heterosystem due to the incorporation of Ge atoms into the Fe3+xSi1−x bottom layer. The resultant lowering of the total free energy caused by the development of the surface roughness results in a transition from an epitaxial to a polycrystalline growth of the upper Fe3+xSi1−x. The average lattice distortion and residual stress of the upper Fe3+xSi1−x were determined by electron diffraction and theoretical calculations to be equivalent to 0.2 GPa for the upper epitaxial layer with a volume misfit of −0.63% compared with a undistorted counterpart. The volume misfit follows the resultant interatomic misfit of |0.42|% with the bottom Ge layer, independently determined by atomic force microscopy. The variation in structural order and morphology significantly changes the magnetic properties of the upper Fe3+xSi1−x layer and leads to a subtle effect on the transport properties of the Ge layer. Both hysteresis loops and FMR spectra differ for the structures with 4 nm and 7 nm Ge layers. The FMR spectra exhibit two distinct absorption lines corresponding to two layers of ferromagnetic Fe3+xSi1−x films. At the same time, a third FMR line appears in the sample with the thicker Ge. The angular dependences of the resonance field of the FMR spectra measured in the plane of the film have a pronounced easy-axis type anisotropy, as well as an anisotropy corresponding to the cubic crystal symmetry of Fe3+xSi1−x, which implies the epitaxial orientation relationship of Fe3+xSi1−x (111)[0−11] || Ge(111)[1−10] || Fe3+xSi1−x (111)[0−11] || Si(111)[1−10]. Calculated from ferromagnetic resonance (FMR) data saturation magnetization exceeds 1000 kA/m. The temperature dependence of the electrical resistivity of a Ge layer with thicknesses of 4 nm and 7 nm is of semiconducting type, which is, however, determined by different transport mechanisms.