Abstract. Ambient ions play an important role in atmospheric processes such as ion-induced new particle formation. While there are several studies of ambient ions for different layers of the atmosphere, data coverage for the free troposphere and especially the upper troposphere and lower stratosphere (UTLS) region is scarce. Here, we present the first airborne measurements of ambient ions using a high-resolution atmospheric pressure interface time-of-flight mass spectrometer (HR-APi-TOF-MS) in the free troposphere and lower stratosphere above Europe on board the HALO aircraft during the CAFE-EU/BLUESKY campaign in May and June 2020. In negative measurement mode, we observed nitrate and hydrogen sulfate and their related ion clusters in an altitude range of 4.7 to 13.4 km. The horizontal profiles for those ions reveal an increasing count rate for NO3- and (HNO3)NO3- towards higher altitudes but no significant trend for HSO4−. From the count rates of the nitrate (NO3-) and hydrogen sulfate (HSO4-) core ions, we inferred the number concentration of gaseous sulfuric acid. The lowest average value was found to be 1.9×105 cm−3 at the maximum altitude bin, i.e. 13.4 km. The highest average value of 7.8×105 cm−3 was observed in the 8.7–9.2 km altitude bin. During the transit through a mixed-phase cloud, we observed an event of enhanced ion count rates and aerosol particle concentrations that can largely be assigned to nitrate ions and particles, respectively; this may have been caused by the shattering of liquid cloud droplets on the surface of the aircraft or the inlet. Furthermore, we report the proof of principle for the measurement of ambient cations and the identification of protonated pyridine.