The structure of Al, Ge, Mo-doped Higher Manganese Silicide (HMS) crystals with the general formulas Mn(Si0.99Ge0.01)(1.75), Mn(Si0.995Ge0.005)(1.75) and (Mn0.98Mo0.02)[(Si0.98Ge0.02)(1.75)](0.99)Al-0.01 was investigated by scanning and transmission electron microscopy, electron diffraction and X-ray energy dispersive spectrometry in a wide scale range from a few mm to several angstrom. Several secondary phases were identified in the Mn4Si7 matrix: Ge1-xSix (0.1 < x < 0.9) solid solution precipitates with Ge concentration ranging from 5 at. % up to 93 at.%, MoSi2 platelets, MnSi and Mn5Si3 precipitates. Their morphology, structure and crystallographic relationships with the HMS matrix were determined. Mostly local strains in the matrix and precipitates due to lattice misfits at interfaces derived from crystallographic relationships were found two orders of magnitude higher than deformation induced by thermal expansion mismatch. Only a few exceptions of specific relationships were found when the lattice misfit and thermal mismatch have close values. The largest misfit of about 22% was observed between MnSi and Mn4Si7 what led to big and numerous cracks in crystals. Therefore, doping can improve the material performance (1) by preventing the formation of MnSi precipitates with metallic properties and (2) by reduction of cracking and crack propagation because of larger MnSi/Mn4Si (7) lattice misfit compared to Ge1-xSix/Mn4Si7 or MoSi2/Mn4Si7 misfits.