A single layer of self-assembled InAs quantum dots was grown on a GaAs (001) substrate by gas source molecular-beam epitaxy. The quantum dots were overgrown with 65 nm GaAs, 25 nm InGaP, and a 10 nm GaAs etch-stop layer. This was either uncapped or capped with 100 nm of low-temperature (LT)-grown, lattice-matched InGaP (LT-InGaP) or with a SiO2 layer or Al2O3 layer. Photoluminescence (PL) measurements were made on samples before and after rapid thermal annealing at 550–900 °C and for 15–120 s at 650 °C. Samples capped with LT-InGaP showed a significant blueshift of the PL peak wavelength for anneals above 575 °C. By comparison, for the SiO2-capped and uncapped samples, the net blueshift only becomes significant for anneals ≫700 °C, while an Al2O3 cap actually reduces the blueshift and suppresses the intermixing. It appears that the best conditions for spatially controlling the quantum dot intermixing occur with annealing at low temperatures (600–650 °C).