The chemistry of Cl2 on a Cu/Si(100) (at relatively high near surface concentrations of Cu) surface has been investigated using X-ray photoelectron spectroscopy (XPS), temperature programmed desorption (TPD), and ion scattering spectroscopy (ISS). XPS and ISS suggested that the deposition of Cu at 120 K on Si(100) resulted in Cu/Si intermixed layers. Heating this surface led to the rapid decrease of Cu in the outermost layer based on ISS, and by 600 K there was no Cu-derived scattering peak even though XPS showed there was a significant amount of Cu in the near surface region. Based on these experimental observations it is postulated that islanding of Cu/Si particles occurred, which is supported by prior studies. Adsorption of Cl2 on the 120 K-Cu deposited Si(100) surface led to some Cu agglomeration, based on XPS. TPD results showed that SiCl4 desorbed from this surface at 530 K and SiCl2 desorbed near 1000 K. The latter peak occurs at the same desorption temperature as SiCl2 for Cl2/Si(100) and is thus attributed to the thermal chemistry of Cl2 on bare Si(100). It is likely, however, that the 530 K desorption feature was a direct result of the weakened surface bonding of Si in Cu/Si islands, compared to Si on bare Si(100).