During the Deep Convective Clouds and Chemistry (DC3) experiment in summer 2012, airborne measurements were performed in the anvil inflow/outflow of thunderstorms over the Central U.S. by three research aircraft. A general overview of Deutsches Zentrum für Luft‐ und Raumfahrt (DLR)‐Falcon in situ measurements (CO, O3, SO2, CH4, NO, NOx, and black carbon) is presented. In addition, a joint flight on 29 May 2012 in a convective line of isolated supercell storms over Oklahoma is described based on Falcon, National Science Foundation/National Center for Atmospheric Research Gulfstream‐V (NSF/NCAR‐GV), and NASA‐DC8 trace species in situ and lidar measurements. During DC3 some of the largest and most destructive wildfires in New Mexico and Colorado state's history were burning, which strongly influenced air quality in the DC3 thunderstorm inflow and outflow region. Lofted biomass burning (BB) plumes were frequently observed in the mid‐ and upper troposphere (UT) in the vicinity of deep convection. The impact of lightning‐produced NOx (LNOx) and BB emissions was analyzed on the basis of mean vertical profiles and tracer‐tracer correlations (CO‐NOx and O3‐NO). On a regular basis DC3 thunderstorms penetrated the tropopause and injected large amounts of LNOx into the lower stratosphere (LS). Inside convection, low O3 air (~80 nmol mol−1) from the lower troposphere was rapidly transported to the UT/LS region. Simultaneously, O3‐rich stratospheric air masses (~100–200 nmol mol−1) were present around and below the thunderstorm outflow and enhanced UT‐O3 mixing ratios significantly. A 10 year global climatology of H2O data from the Aura Microwave Limb Sounder confirmed that the Central U.S. is a preferred region for convective injection into the LS.