The CopterSonde is an unmanned aircraft system (UAS) developed in house by a team of engineers and meteorologists at the University of Oklahoma. The CopterSonde is an ambitious attempt by the Center for Autonomous Sensing and Sampling to address the challenge of filling the observational gap present in the lower atmosphere among the currently used meteorological instruments such as towers and radiosondes. The CopterSonde is a unique and highly flexible platform for in situ atmospheric boundary layer measurements with high spatial and temporal resolution, suitable for meteorological applications and research. Custom autopilot algorithms and hardware features were developed as solutions to problems identified throughout several field experiments carried out since 2017. In these field experiments, the CopterSonde has been proven capable of safely operating at wind speeds up to 22 m s−1, flying at 3050 m above mean sea level, and operating in extreme temperatures: nearly −20 ∘C in Finland and 40 ∘C in Oklahoma, United States. Leveraging the open-source ArduPilot autopilot code has allowed for seamless integration of custom functions and protocols for the acquisition, storage, and distribution of atmospheric data alongside the flight control data. This led to the development of features such as the “wind vane mode” algorithm, which commands the CopterSonde to always face into the wind. It also inspired the design of an asymmetric airframe for the CopterSonde, which is shown to provide more suitable locations for weather sensor placement, in addition to allowing for improvements in the overall aerodynamic characteristics of the CopterSonde. Moreover, it has also allowed the team to design and create a modular shell where the sensor package is attached and which can run independently of the CopterSonde’s main body. The CopterSonde is on the trend towards becoming a smart UAS tool with a wide possibility of creating new adaptive and optimized atmospheric sampling strategies.