Abstract Acoustic waves generated by seismic waves contain information on the internal structure of planets, and can be sensed by pressure sensors onboard high-altitude balloons. To identify the various contributions (infrasound signal, noise, balloon response, etc.) in such pressure records, a full waveform modeling is implemented and completed by infrasound ray tracing and additional data analysis. Here, we analyze the Stratéole-2 pressure data associated with two earthquakes (Garcia et al. Geophys. Res. Lett. 49(15):e98844, 2022) and compared these to full waveform simulations by SPECFEM2D-DG-LNS software. Even if our simulations do not precisely reproduce the waveform observed in the frequency range [0.05, 0.3] Hz, we show that the waveform presents more sensitivity to quake and internal structure parameters than to atmospheric structure, and that seismic surface wave dispersion is observed in balloon pressure records. The long-duration pressure oscillations observed after the main infrasonic signal cannot be fully reproduced by our one-dimensional input model even when source time function complexity and aftershocks are considered. These features are ascribed mainly to the complex vertical ground movements below the balloon and partly to late secondary infrasound arrivals excited by the interactions of seismic waves with the topography. These results enhance the advantages and limitations of quake-related infrasound observations on board terrestrial and planetary balloon platforms. Graphical Abstract