In this work, we used a Zeppelin NT equipped with six sensor setups, each composed of four different low-cost electrochemical sensors (ECSs) to measure nitrogen oxides (NO and NO2), carbon monoxide, and Ox (NO2+O3) in Germany. Additionally, a MIRO MGA laser absorption spectrometer was installed as a reference device for in-flight evaluation of the ECSs. We report not only the influence of temperature on the NO and NO2 sensor outputs but also find a shorter timescale (1 s) dependence of the sensors on the relative humidity gradient. To account for these dependencies, we developed a correction method that is independent of the reference instrument. After applying this correction to all individual sensors, we compare the sensor setups with each other and to the reference device. For the intercomparison of all six setups, we find good agreements with R2≥0.8 but different precisions for each sensor in the range from 1.45 to 6.32 ppb (parts per billion). The comparison to the reference device results in an R2 of 0.88 and a slope of 0.92 for NOx (NO+NO2). Furthermore, the average noise (1σ) of the NO and NO2 sensors reduces significantly from 6.25 and 7.1 to 1.95 and 3.32 ppb, respectively. Finally, we highlight the potential use of ECSs in airborne applications by identifying different pollution sources related to industrial and traffic emissions during multiple commercial and targeted Zeppelin flights in spring 2020. These results are a first milestone towards the quality-assured use of low-cost sensors in airborne settings without a reference device, e.g., on unmanned aerial vehicles (UAVs).