In recent years, non-thermal atmospheric pressure plasmas have been used extensively for surface treatments, in particular, due to their potential in biological applications. However, the scientific results often suffer from reproducibility problems due to unreliable plasma conditions as well as complex treatment procedures. To address this issue and provide a stable and reproducible plasma source, the COST-Jet reference source was developed. In this work, we propose a detailed protocol to perform reliable and reproducible surface treatments using the COST reference microplasma jet (COST-Jet). Common issues and pitfalls are discussed, as well as the peculiarities of the COST-Jet compared to other devices and its advantageous remote character. A detailed description of both solid and liquid surface treatment is provided. The described methods are versatile and can be adapted for other types of atmospheric pressure plasma devices.