In recent decades, there have been major advancements in atmospheric in-situ measurement techniques, expanding our ability to monitor greenhouse gas concentrations. One such development has been in the application of non-dispersive infrared (NDIR) technology. This technology and the sensors that utilize it have greatly improved, in precision and stability, which has subsequently resulted in their rapid and broad deployment to quantify greenhouse gas concentrations near Earth’s surface. Despite this popularity, one field that has not seen the adoption of NDIR technology is in-situ balloon-based measurements, due in part to the challenging environmental conditions. The Canadian Atmospheric Laser Absorption Spectrometer Experiment Test-bed (CALASET) is a project that is dedicated to designing, building and utilizing novel balloon-borne instruments. Presented here is the design and calibration of CALASET-SE, an innovative instrument adapting commercial NDIR technology to make in-situ measurements of CO2 and H2O concentrations across a range of temperature and pressure conditions at altitudes ranging from the surface to the middle stratosphere. In June 2024, CALASET-SE was launched from Kiruna, Sweden by Centre National D'études Spatiales (CNES) as part of their first long duration trans-Atlantic stratospheric balloon flight which traversed the North Atlantic Ocean and landed on Baffin Island, Canada. The flight was a collaborative project between CNES, the Swedish Space Corporation (SSC), and Canadian Space Agency (CSA) that brought together scientists from Canada, France, Germany and Sweden to test their instruments in the stratosphere. The design of the instrument will be discussed, including the implementation and adaptation of the NDIR sensor, and performance and calibration tests conducted before the flight.