Poly-ether-ether-ketone (PEEK) is an aesthetically pleasing natural material with good biocompatibility and shock absorption characteristics. The application of PEEK as a dental implant or abutment is expected to reduce the risk of failure and enhance aesthetics. Given that approximately one in 15 patients have allergic reactions to antibiotics, photodynamic therapy (PDT) has been gaining attention as an alternative treatment. Herein, the applicability of PEEK dental implants or abutments was investigated using material analyses, biofilm formation assay, and cell viability tests. The possible use of PDT for peri-implant mucositis was evaluated with the biofilm removal assay. The obtained data were analyzed based on the multivariate analysis of variance, paired t-tests, and the Pearson correlation coefficient (α = 0.05). The results revealed that PEEK was significantly less conducive to the formation of biofilms with S. mutans and A. actinomycetemcomitan (p < 0.001) but exhibited comparable MG-63 (human osteoblast-like) osteoblast cell viability (p > 0.05) to the other materials. PDT had similar antimicrobial efficacy and yielded similar biofilm removal effects to antibiotics. Altogether, these findings suggest that PEEK has attractive features and can serve as an alternative material for dental implants or abutments. In cases where peri-implant mucositis occurs, PDT can be used as an accessible therapeutic approach.