Intrinsic bioinertness severely hampers the application of polyetheretherketone (PEEK), although in the, field of dentistry it is considered to be an ideal titanium substitute implanting material. In this study, a bioactive silicate coating, was successfully introduced onto PEEK surface by using electron beam evaporation (EBE) technology to improve its bioactivity and osseointegration of PEEK. Through controlling the duration of EBE, the incorporated amounts of silicon (Si) could be exquisitely adjusted to obtain proper biofunctionality, as assessed by cell adhesion, proliferation, osteogenic gene expression, and protein detection. In vivo, the samples were then tested in a femur implantation model to assay osseointegration effects in ovariectomized (OVX) rats. Remarkable enhancement of adhesion, spreading, osteogenesis, and differentiation of bone marrow stem cells (rBMSCs-OVX) were noted on silicate-coated samples. In particular, the group that was processed for 5 min with EBE (EBB-5 min) showed the most improvements in ALP activity and osteogenic-related gene expression compared to the remaining groups. Better osseointegration of the group that was processed for 8 min with EBE (EBE-8 min) was observed in vivo, as indicated by micro-CT test, fluorescent labeling, and histological and histomorphometric analyses. Collectively, the outcomes of the above experiments demonstrate that the present work is a meaningful attempt to promote osseointegration under osteoporotic conditions with only Si element incorporated to PEEK Surface by the application of EBE technique. To the best of our knowledge, this work is the first demonstration of tuning the surface properties of PEEK via the adoption of an EBE-fabricated silicate coating to address an osteoporotic problem both in vitro and in vivo.