Abstract This study investigated two of the most commonly used CAD–CAM materials for patient-specific reconstruction in craniomaxillofacial surgery. The aim of this study was to access the biofilm formation of Staphylococcus aureus, Streptococcus mutans, Enterococcus faecalis, and Escherichia coli on titanium and PEEK medical implant materials. Two titanium specimens (titanium grade 2 tooled with a Planmeca CAD–CAM milling device and titanium grade 5 tooled with a computer-aided design direct metal laser sintering device (CAD-DMLS)) and one PEEK specimen tooled with a Planmeca CAD–CAM milling device were studied. Bacterial adhesion on implants was evaluated in two groups (saliva-treated group and non-saliva-treated group) to imitate intraoral and extraoral surgical routes for implant placement. The PEEK medical implant material showed higher bacterial adhesion by S. aureus, S. mutans, and E. coli than titanium grade 2 and titanium grade 5, whereas E. faecalis showed higher adhesion to titanium as compared to PEEK. Saliva contamination of implants also effected bacterial attachment. Salivary coating enhanced biofilm formation by S. aureus, S. mutans, and E. faecalis. In conclusion, our findings imply that regardless of the implant material type or tooling techniques used, salivary coating plays a vital role in bacterial adhesion. In addition, the majority of the bacterial strains showed higher adhesion to PEEK than titanium.