Under controlled irradiation of low energy carbon ions, photoluminescence (PL) study of InAs quantum dots prepared with different capping structures (GaAs and InAlGaAs) was carried out. Samples were investigated by varying implantation energy from 15 keV to 50 keV with fluence ranging between 3 × 1011ions/cm2 and 8 × 1011 ions/cm2. For fixed fluence of 4 × 1011ions/cm2, low temperature PL showed enhancement in a certain range of energy, along with a blue shift in the PL peak wavelength. In contrast, with varying fluence at fixed implantation energy of 50 keV, PL enhancement was not significant, rather a drop in PL intensity was noted at higher fluence from 5 × 1011 to 8 × 1011 ions/cm2. Moreover, carbon ion implantation caused a blue shift in the PL emission peak for both energy and fluence variations. PL intensity suppression was possibly caused by the formation of non-radiative recombination centers (NRCs) near the capping layer, while the corresponding blue shift might be attributed to stress generation in the capping layer due to implantation. As-grown and implanted InAlGaAs capped samples did not exhibit much variation in full width at half maxima of PL spectra; however, significant variation was observed for the GaAs capped sample. These results validate that InAlGaAs-capped QDs are more immune to ion implantation.