Tissue engineering can benefit from wide variety of materials produced by microorganisms. Natural origin materials often possess good biocompatibility, biodegradability with sustainable production by microorganisms. A phytoplankton, diatom, produces an amorphous silica shell that can be obtained by a cost efficient production process. Diatom shells (DS) are promising for bone tissue engineering since silicon enhances bone regeneration. Biocompatible and biodegradable biopolymers with microorganism origin can be combined with DS to produce tissue engineering constructs. In this study, a novel multifunctional 3D fibrous scaffold for bone tissue engineering was produced by co-electrospinning system; antibiotic loaded poly(hydroxybutyrate-co-hydroxyvalerate)/poly(ε-caprolactone) (PHBV/PCL) fibers and DS incorporated pullulan (PUL) fibers. Controlled release of cefuroxime axetil (CA) from DS and scaffolds were investigated upon loading CA into DS or PHBV/PCL fibers. Purified DS were characterized with ESCA, SEM, and EDX analyses while scaffolds were evaluated in terms of morphology, porosity, degradation, calcium deposition, water retention and mechanical properties. In vitro studies showed that scaffolds bearing DS have improved human osteosarcoma (Saos-2) cell viability. Developed co-electrospun scaffold showed higher osteocompatibility with better cell spreading and cell distribution. Results showed that DS loaded, co-electrospun scaffold having both hydrophobic and hydrophilic characteristics can be a promising biomaterial for bone tissue engineering.