This dataset contains magnetometry data and design files related to testing of new drone-based magnetometer configurations and magnetic compensation software. Data were collected in Santa Cruz (CA) in September 2020 to compare two magnetometer systems that are flown with Unmanned Aerial Systems (UAS). Each system was flown using different suspension designs. To compare the systems and to characterize noise levels of the systems, calibration patterns and dense grid surveys were flown with each configuration. This dataset was further used to test magnetic compensation software. The overall aim of this study was to compare the variability of different UAS-based magnetometry systems that can be used for geophysical surveying. The dataset includes comma-separated values (CSV) formatted files, CAD design files (STL), as well as RAW data files downloaded directly from the magnetometers, that can be converted to CSV format utilizing software tools provided by the magnetometer manufacturers.