Space observatories for gravitational radiation such as LISA are equipped with dedicated on-board instrumentation capable of measuring magnetic fields with low-noise conditions at millihertz frequencies. The reason is that the core scientific payload can only operate successfully if the magnetic environment meets certain strict low-frequency requirements. With this purpose, a simplified version of the proposed magnetic measurement system for LISA has been developed for a six-unit CubeSat, which will make it possible to improve the technology readiness level (TRL) of the instrument. The special feature of the experiment is that the magnetic sensors integrated in the payload are magnetically shielded to low-frequency fluctuations by using a small cylindrical permalloy enclosure. This will allow the in-flight noise characterization of the system under the CubeSat orbit environment. Therefore, a CubeSat platform will offer the opportunity to measure the capability of the instrument and will guide the progress towards the improved magnetic measurement system for LISA. This article describes the principal characteristics and implementation of the CubeSat payload.