Mn2GeSe4 is Spinel-like structured and crystallizes in the orthorhombic Pnma space group. There are two inequivalent Mn sites. In the first Mn site, Mn(1) is bonded to one Se(2), one Se(3), and four equivalent Se(1) atoms to form MnSe6 octahedra that share corners with four equivalent Mn(1)Se6 octahedra, corners with four equivalent Mn(2)Se6 octahedra, corners with four equivalent Ge(1)Se4 tetrahedra, edges with two equivalent Mn(2)Se6 octahedra, and  an edgeedge with one Ge(1)Se4 tetrahedra. The corner-sharing octahedral tilt angles range from 47-56°. In the second Mn site, Mn(2) is bonded to two equivalent Se(1), two equivalent Se(2), and two equivalent Se(3) atoms to form MnSe6 octahedra that share corners with four equivalent Mn(1)Se6 octahedra, corners with two equivalent Ge(1)Se4 tetrahedra, edges with two equivalent Mn(1)Se6 octahedra, edges with two equivalent Mn(2)Se6 octahedra, and edges with two equivalent Ge(1)Se4 tetrahedra. The corner-sharing octahedral tilt angles range from 50-56°. Ge(1) is bonded to one Se(2), one Se(3), and two equivalent Se(1) atoms to form GeSe4 tetrahedra that share corners with two equivalent Mn(2)Se6 octahedra, corners with four equivalent Mn(1)Se6 octahedra,  an edgeedge with one Mn(1)Se6 octahedra, and edges with two equivalent Mn(2)Se6 octahedra. The corner-sharing octahedral tilt angles range from 58-62°. There are three inequivalent Se sites. In the first Se site, Se(1) is bonded in a rectangular see-saw-like geometry to one Mn(2), two equivalent Mn(1), and one Ge(1) atom. In the second Se site, Se(2) is bonded in a rectangular see-saw-like geometry to one Mn(1), two equivalent Mn(2), and one Ge(1) atom. In the third Se site, Se(3) is bonded to one Mn(1), two equivalent Mn(2), and one Ge(1) atom to form distorted corner-sharing SeMn3Ge trigonal pyramids.
Mn2GeSe4 is Spinel-like structured and crystallizes in the orthorhombic Pnma space group. There are two inequivalent Mn sites. In the first Mn site, Mn(1) is bonded to one Se(2), one Se(3), and four equivalent Se(1) atoms to form MnSe6 octahedra that share corners with four equivalent Mn(1)Se6 octahedra, corners with four equivalent Mn(2)Se6 octahedra, corners with four equivalent Ge(1)Se4 tetrahedra, edges with two equivalent Mn(2)Se6 octahedra, and  an edgeedge with one Ge(1)Se4 tetrahedra. The corner-sharing octahedral tilt angles range from 47-56°. The Mn(1)-Se(2) bond length is 2.67 Å. The Mn(1)-Se(3) bond length is 2.73 Å. There are two shorter (2.75 Å) and two longer (2.77 Å) Mn(1)-Se(1) bond lengths. In the second Mn site, Mn(2) is bonded to two equivalent Se(1), two equivalent Se(2), and two equivalent Se(3) atoms to form MnSe6 octahedra that share corners with four equivalent Mn(1)Se6 octahedra, corners with two equivalent Ge(1)Se4 tetrahedra, edges with two equivalent Mn(1)Se6 octahedra, edges with two equivalent Mn(2)Se6 octahedra, and edges with two equivalent Ge(1)Se4 tetrahedra. The corner-sharing octahedral tilt angles range from 50-56°. Both Mn(2)-Se(1) bond lengths are 2.75 Å. Both Mn(2)-Se(2) bond lengths are 2.71 Å. Both Mn(2)-Se(3) bond lengths are 2.70 Å. Ge(1) is bonded to one Se(2), one Se(3), and two equivalent Se(1) atoms to form GeSe4 tetrahedra that share corners with two equivalent Mn(2)Se6 octahedra, corners with four equivalent Mn(1)Se6 octahedra,  an edgeedge with one Mn(1)Se6 octahedra, and edges with two equivalent Mn(2)Se6 octahedra. The corner-sharing octahedral tilt angles range from 58-62°. The Ge(1)-Se(2) bond length is 2.38 Å. The Ge(1)-Se(3) bond length is 2.34 Å. Both Ge(1)-Se(1) bond lengths are 2.38 Å. There are three inequivalent Se sites. In the first Se site, Se(1) is bonded in a rectangular see-saw-like geometry to one Mn(2), two equivalent Mn(1), and one Ge(1) atom. In the second Se site, Se(2) is bonded in a rectangular see-saw-like geometry to one Mn(1), two equivalent Mn(2), and one Ge(1) atom. In the third Se site, Se(3) is bonded to one Mn(1), two equivalent Mn(2), and one Ge(1) atom to form distorted corner-sharing SeMn3Ge trigonal pyramids.