Copper indium diselenide (CIS) nanoparticles were synthesized using a microwave-assisted one-pot solvothermal approach. For these studies high microwave-absorbing precursors were used in combination with low microwave absorbing solvents tri-n-octylphosphine (TOP) and oleic acid (OA) to investigate the effect of selective heating of the precursors on nanoparticle synthesis. High-resolution transmission electron microscopy (TEM) results indicated that the nanoparticles were spherical, crystalline and 4–5 nm in diameter. X-ray diffraction (XRD) results indicated that the nanoparticles had a body-centered tetragonal structure with planar defects that decreased in concentration with increasing reaction temperature and reaction time. The nanoparticle compositions varied depending on the reaction conditions and the compositions were found to approach stoichiometry for increased reaction times. Fourier transform infrared (FTIR) spectroscopy indicated both solvents adsorbed to the nanoparticle surface and energy dispersive spectroscopy indicated that these ligands became chlorinated during the reaction. The uniform temperature profile offered by the microwave heating allowed for highly reproducible batch-to-batch reactions, allowing for tight control over composition and defect concentration.