This study evaluated the influence of light quality and intensity during healing and acclimatization on the CO₂ exchange rate, growth, and morphogenesis of grafted pepper (Capsicum annuum L.) transplants, using a system for the continuous measurement of the CO₂ exchange rate. C. annuum L. ‘Nokkwang’ and ‘Tantan’ were used as scions and rootstocks, respectively. Before grafting, the transplants were grown for four weeks in a growth chamber with artificial light, where the temperature was set at 25/18℃ (light/dark period) and the light period was 14 hours·d -1 . The grafted pepper transplants were then healed and acclimatized under different light quality conditions using fluorescent lamps (control) and red, blue, and red + blue light-emitting diodes (LEDs). All the transplants were irradiated for 12 hours per day, for six days, at a photosynthetic photon flux (PPF) of 50, 100, or 180 μmol·m -2 ·s -1 . The higher PPF levels increased the CO₂ exchange rate during the healing and acclimatization. A smaller increase in the CO₂ exchange rates was observed in the transplants under red LEDs. At a PPF of 180 μmol·m -2 ·s -1 , the CO₂ exchange rate of the transplants irradiated with red LEDs was lowest and it was 37% lower than those irradiated with fluorescent lamps. The CO₂ exchange rates of transplants irradiated with blue LEDs was the highest and 20% higher than those irradiated under fluorescent lamps. The graft take was not affected by the light quality. The grafted pepper transplants irradiated with red LEDs had a lower SPAD value, leaf dry weight, and dry matter content. The transplants irradiated with blue LEDs had longer shoot length and heavier stem fresh weight than those irradiated with the other treatments. Leaves irradiated with the red LED had the smallest leaf area and showed leaf epinasty. In addition, the palisade and spongy cells of the pepper leaves were dysplastic and exhibited hyperplasia. Grafted pepper transplants treated with red + blue LEDs showed similar growth and morphology to those transplants irradiated with fluorescent lamps. These results suggest that high-quality grafted pepper transplants can be obtained by healing and acclimatization under a combination of blue and red lights at a high PPF level.