Mn5NiN4 crystallizes in the orthorhombic Pmmn space group. There are two inequivalent Mn sites. In the first Mn site, Mn(1) is bonded in a 3-coordinate geometry to one N(1) and two equivalent N(2) atoms. In the second Mn site, Mn(2) is bonded in a 4-coordinate geometry to two equivalent N(1) and two equivalent N(2) atoms. Ni(1) is bonded in a bent 120 degrees geometry to two equivalent N(1) atoms. There are two inequivalent N sites. In the first N site, N(1) is bonded to one Mn(2), two equivalent Mn(1), and one Ni(1) atom to form NMn3Ni tetrahedra that share corners with two equivalent N(1)Mn3Ni tetrahedra and corners with six equivalent N(2)Mn5 trigonal bipyramids. In the second N site, N(2) is bonded to one Mn(2) and four equivalent Mn(1) atoms to form distorted NMn5 trigonal bipyramids that share corners with six equivalent N(1)Mn3Ni tetrahedra,  a cornercorner with one N(2)Mn5 trigonal bipyramid, and edges with two equivalent N(2)Mn5 trigonal bipyramids.
Mn5NiN4 crystallizes in the orthorhombic Pmmn space group. There are two inequivalent Mn sites. In the first Mn site, Mn(1) is bonded in a 3-coordinate geometry to one N(1) and two equivalent N(2) atoms. The Mn(1)-N(1) bond length is 1.82 Å. There is one shorter (1.89 Å) and one longer (2.00 Å) Mn(1)-N(2) bond length. In the second Mn site, Mn(2) is bonded in a 4-coordinate geometry to two equivalent N(1) and two equivalent N(2) atoms. Both Mn(2)-N(1) bond lengths are 1.85 Å. Both Mn(2)-N(2) bond lengths are 1.96 Å. Ni(1) is bonded in a bent 120 degrees geometry to two equivalent N(1) atoms. Both Ni(1)-N(1) bond lengths are 1.81 Å. There are two inequivalent N sites. In the first N site, N(1) is bonded to one Mn(2), two equivalent Mn(1), and one Ni(1) atom to form NMn3Ni tetrahedra that share corners with two equivalent N(1)Mn3Ni tetrahedra and corners with six equivalent N(2)Mn5 trigonal bipyramids. In the second N site, N(2) is bonded to one Mn(2) and four equivalent Mn(1) atoms to form distorted NMn5 trigonal bipyramids that share corners with six equivalent N(1)Mn3Ni tetrahedra,  a cornercorner with one N(2)Mn5 trigonal bipyramid, and edges with two equivalent N(2)Mn5 trigonal bipyramids.