Air pollution, besides being one of the leading causes of death worldwide, remains one of the most controversial topics in environmental monitoring. The current state of the art refers to remote satellite analysis and static ground-level technologies. The O-ZONE project has set itself the objective of bridging this technological gap using dynamic in situ analysis using compact, inexpensive and reusable samplers that can be integrated onboard stratospheric balloons and drones. The prototype, therefore, consists of a pneumatic system, a set of filters and a sampling bag. Thanks to this architecture, it is possible to sample atmospheric air at different altitudes. After the flight, the samples collected are analysed using chromatographic techniques to provide a picture of the various air layers. On 30 September 2021, the fully autonomous payload successfully flew in Kiruna (Swedish Lapland) aboard BEXUS 30, the stratospheric balloon made available by the promoters of the “hands-on” project of the same name, SNSA (Swedish National Space Agency), DLR (Deutsches Zentrum für Luft- und Raumfahrt) and ESA (European Space Agency). In this paper, the technical specifications of the device are described, with a focus on the sampling system; we then highlight the results obtained by the filters that, at different altitudes, collected stratospheric pollutants such as VOCs and, in the first layers of the atmosphere, PM. In conclusion, an interpretation of the results is provided to better understand the possible future uses of the prototype.