Abstract In this study, we have examined the impact of droughts on the atmospheric CO2 spatial variability and changes its emission scenario over India. Surface monitoring over India is very sparse and have started recently. Satellite retrievals from AIRS/Aqua during 2004–2011 are used here to understand CO2 variability over India. During recent decade, Indian region witnessed two drought years 2004 and 2009 and no flood. Year 2009 was mega drought for India ever seen, when actual rainfall was approx −23% below the mean rainfall over most part of India. Satellite retrieved mid-tropospheric CO2 indicates increase of about 3 ppm during summer monsoon drought. Enhanced impact of drought conditions is also seen on subsequent seasons, winter (JF) and hot pre-monsoon season (MAM). Post-monsoon season (OND) does not show any clear impact, as rainfall during this season has its own variability quite different than summer monsoon (JJAS) may be compensating changes in CO2 values. Decrease in vegetation and weak circulation patterns during drought conditions may have influences on distribution of CO2 over Indian region.