In addition to offering a wide range electrical, optical and magnetic properties, oxide nanostructures can be stable in a range of environments without needing to add protective layers. In this work, we have observed the formation of self-assembled oxidized-copper nanodots on the SrTiO3(100) substrate using oxygen plasma assisted molecular beam epitaxy. The composition and structure were examined by x-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy, x-ray diffraction, and scanning probe microscopy in a wide range of growth parameters (temperature, oxygen pressure, and Cu flux). Under different growth conditions different shapes and/or composition have been found: truncated dots, square pyramids, and multifaceted domes with composition to be Cu2O or containing Cu metal also. Since nanostructure composition changes with temperature, observation made by interrupting growth and cooling may not be adequate. Thus, in addition to scanning probe measurements in ambient conditions, XPS spectra have been acquired at elevated temperatures in step-by-step mode at different stages of nanodots formation. Observed correlations between structural and composition changes will be discussed. Understanding of the evolution of the dot shape, size and composition would allow us to optimize formation conditions to synthesize cooper oxide nanodots with desirable parameters.@footnote 1@ @FootnoteText@ @footnote 1@ This work has been conducted as part of the PNNL Nanoscience and Nanotechnology Initiative supported by the Office of Biological and Environmental Research, U. S. Department of Energy.