Regarding the dynamic development of 3D printing technology, as well as its application in a growing part of industries, i.e., in the automotive industry, construction industry, medical industry, etc., there is a notable opportunity for its application in producing dental implants, which presents a promising alternative to traditional implant manufacturing methods. The medical industry is very restrictive regarding the applied materials, and it is necessary to use materials that exhibit very good mechanical and thermal parameters, show clinical indifference and biocompatibility, are non-allergenic and non-cancerous, and are likely to sterilize. Such materials are poly(aryl-ether-ketone)s (PAEK)s, mainly poly(ether-ether-ketone) (PEEK) and poly(ether-ketone-ketone) (PEKK), that are found to be high-performance polymers and can be defined as materials that retain their functionality even in extreme conditions. In the present paper, two types of PEEKs and PEKK were compared regarding their structural, mechanical, and thermal properties along with the biological activity toward selected strains. The tested samples were obtained with Fused Deposition Modeling (FDM) technology. The PEKK, after heat treatment, exhibits the most promising mechanical properties as well as less bacterial adhesion on its surface when compared to both PEEKs. Consequently, among the evaluated materials, PEKK after heat treatment stands out as the optimal selection for a dental prosthesis.