InAs self-assembled quantum dots (QDs) were grown by molecular beam epitaxy on (001) GaAs substrate. Uncapped and capped QDs with GaAs and graphene layers were studied using atomic force microscopy and Raman spectroscopy. Graphene multi-layer was grown by chemical vapor deposition and transferred on InAs/GaAs QDs. It is well known that the presence of a cap layer modifies the size, shape, and density of the QDs. According to the atomic force microscopy study, in contrast to the GaAs capped sample, which induce a dramatic decrease of the density and height of dots, graphene cap layer sample presents a slight influence on the surface morphology and the density of the islands compared with the uncapped one. The difference shown in the Raman spectra of the samples is due to change of strain and alloy disorder effects on the QDs. Residuals strain and the relaxation coefficients have been investigated. All results confirm the best crystalline quality of the graphene cap layer dots sample relative to the GaAs capped one. So graphene can be used to replace GaAs in capping InAs/GaAs dots. To our knowledge, such study has not been carried out until now. Copyright © 2013 John Wiley & Sons, Ltd.