Because of its useful optoelectronic properties and the relative abundance of its elements, the quaternary semiconductor Cu2ZnSnS4 (CZTS) has garnered considerable interest in recent years. In this work, we dope divalent, high spin transition metal ions (M2+ = Mn2+, Co2+, Ni2+) into the tetrahedral Zn2+ sites of wurtzite CZTS nanorods. The resulting Cu2MxZn1–xSnS4 (CMTS) nanocrystals retain the hexagonal crystalline structure, elongated morphology, and broad visible light absorption profile of the undoped CZTS nanorods. Electron paramagnetic resonance (EPR), X-ray photoelectron spectroscopy (XPS), and infrared (IR) spectroscopy help corroborate the composition and local ion environment of the doped nanocrystals. EPR shows that, similarly to MnxCd1–xSe, washing Cu2MnxZn1–xSnS4 nanocrystals with trioctylphosphine oxide (TOPO) is an efficient way to remove excess Mn2+ ions from the particle surface. XPS and IR of as-isolated and thiol-washed samples show that, in contrast to binary chalcogenides, Cu2MnxZn1–xSnS4nanocrystals aggregate not through dichalcogenide bonds, but through excess metal ions cross-linking the sulfur-rich surfaces of neighboring particles. Our results may help in expanding the synthetic applicability of CZTS and CMTS materials beyond photovoltaics and into the fields of spintronics and magnetic data storage.