Silicon pore optics are a new type of high-performance x-ray optics designed to enable future space-borne x-ray observatories such as European Space Agency’s Athena. These optics will make it possible to build telescopes with effective areas of the order of a few square meters and angular resolutions better than 5 s of arc. During manufacturing of the optics, thin film metallic coatings are sputtered onto mirror plates to help achieve this large effective area. Then, these plates are stacked on top of each other using direct silicon bonding to achieve the shape of an approximate Wolter type-I telescope design. It is, therefore, necessary to verify the compatibility of the coating and bonding processes. We observe the unintentional removal of coatings on silicon pore optics plates after their wet chemical activation, a step required to make direct bonding possible. In this paper, we investigate plasma etching prior to thin film deposition as a solution to this problem. First, we ensure that plasma etching does not impact the low surface roughness required to achieve high imaging performance. Then, we demonstrate that plasma etching before thin film deposition prevents unintentional removal of the metallic coatings during the activation step, making coating deposition compatible with direct bonding of silicon pore optics plates.