Polyether ether ketone (PEEK) is a three-dimensional (3D)-printable material with excellent mechanical properties for bone replacement implants. However, bioactivation is needed to improve its osseointegration. Plasma immersion ion implantation (PIII) provides PEEK surfaces with a high density of radicals, improving hydrophilicity and enabling covalent bonds with biological molecules. On the PIII-treated surface, amorphous calcium phosphate-associated protein depositions form a strongly bonded, mineralised layer during incubation in a cell culture medium. The strong adhesion is attributed to covalent linking of protein to the PEEK surface, which cannot be achieved by improved hydrophilicity or the introduction of functional groups alone. After 3D-printed porous PEEK scaffolds were PIII-treated, osteoblast-like cell attachment increased by 8.8%, proliferation rate increased by 27% and mineralisation was enhanced, encouraging rapid osseointegration of patient-specific implants.