Increasingly, self-assembled quantum dots produced by the Stranski-Krastanov growth mode during molecular beam epitaxy are being used for both photonic and electronic devices. In order to fully realize the potential of these nanostructures, control of both the quantum dot size and the density distributions is very important. In addition, the ability to tune the confined energy states will enhance the ability to exploit these nanostructures. Herein, we report on the structural modifications induced by annealing dots under dissimilar anion fluxes. Such strain and chemical tuning enabled by annealing can be used as a means of further controlling quantum dots properties.