Atmospheric concentrations of the greenhouse gases carbon dioxide and nitrous oxide have increased substantially because of human activities. However, their sources in South Asia, which contribute strongly to the accelerating global growth of carbon dioxide and nitrous oxide, are poorly quantified. Here, we present aircraft measurements with high temporal and vertical resolution up to 20 km during the Asian summer monsoon where rapid upward transport of surface pollutants to greater altitudes occurs. Using Lagrangian model simulations, we successfully reconstruct observed carbon dioxide profiles leading to an improved understanding of the vertical structure of carbon dioxide in the Asian monsoon region. We show that spatio-temporal patterns of carbon dioxide on the Indian subcontinent driven by regional flux variations rapidly propagate to approximately 13 km with slower ascent above. Enhanced carbon dioxide compared to the stratospheric background can be detected up to 20 km. We suggest that the propagation of these signals from the surface to the stratosphere can be used to evaluate transport models and assess carbon dioxide fluxes in South Asia.