Atomically precise thiolate-protected coinage metal nanoclusters and their alloys are far more numerous than their selenium congeners, the synthesis of which remains extremely challenging. Herein, we report the synthesis of a series of atomically defined dithiophosph(in)ate protected eight-electron superatomic palladium silver nanoalloys [PdAg20{S2PR2}12], 2a–c (where R = OiPr, a; OiBu, b; Ph, c) via ligand exchange and/or co-reduction methods. The ligand exchange reaction on [PdAg20{S2P(OnPr)2}12], 1, with [NH4{Se2PR2}12] (where R = OiPr, or OnPr) leads to the formation of [PdAg20{Se2P(OiPr)2}12] (3) and [PdAg20{Se2P(OnPr)2}12] (4), respectively. Solid state structures of 2a, 2b, 3 and 4 unravel different PdAg20 metal frameworks from their parent cluster, originating from the different distributions of the eight-capping silver(I) atoms around a Pd@Ag12 centered icosahedron with C2,D3,Th and Th symmetries, respectively. Surprisingly ambient temperature crystallization of the reaction product 3 obtained by the ligand exchange reaction on 1 has resulted in the co-crystallization of two isomers in the unit cell with overall T (3a) and C3 (3b) symmetries, respectively. To our knowledge, this is the first ever characterized isomeric pair among the selenolate-protected NCs. Density functional theory (DFT) studies further rationalize the preferred geometrical isomerism of the PdAg20 core.