Purpose Synthetic polymers such as poly(lactic acid) (PLA) are well suited for preparing patient-specific bone tissue scaffolds by three-dimensional (3D) printing due to their favorable mechanical properties; however, they have limited biological activity. Natural polymers have good bioactivity and provide a better cellular microenvironment for attachment, proliferation, and differentiation, but lack the mechanical strength required as a bone substitute. Method In this work, porous PLA scaffolds were prepared by fused filament fabrication. For uniform cell seeding and enhanced cellular function, a silk fibroin-alginate (SF/Alg) blend hydrogel loaded with human mesenchymal cells (hMSCs) was loaded into the pores of the 3D-printed hybrid scaffolds between the struts. The physicochemical properties of the scaffold and the hMSC response were characterized. Results The gel-loaded 3D-printed PLA scaffolds were stable over 21 days in an aqueous buffer solution. The compressive strength of the scaffolds was approximate to 10 MPa, which is similar to that of cancellous bone. The proliferation and viability of hMSCs were significantly enhanced when loaded within the SF/Alg hydrogel in the PLA scaffolds than in the neat PLA scaffold. Furthermore, the stem cells in the gel-loaded 3D-printed PLA scaffold showed markedly higher alkaline phosphatase expression and calcium phosphate deposition, which indicates higher osteogenic differentiation with the gels. These observations were corroborated by increased expressions of osteocalcin, RUNX2, and BMP-2. Conclusion Thus, the combination of SF/Alg hydrogel loaded with stem cells offers a promising route for enhancing the bioactivity of 3D-printed PLA scaffolds with significant clinical potential for bone tissue engineering. Owing to their good mechanical stability, 3D-printed porous scaffolds of thermoplastics such as PLA have been used for bone tissue engineering applications. However, the presence of macro-sized pores leads to low cell attachment efficiency and distribution within the scaffolds, which results in low osteogenic activity. In this work, stem cells were encapsulated within the sonicated silk fibroin and alginate blend hydrogel and embedded within the gaps of 3D-printed PLA struts. This hybrid approach maximizes the cell density and uniform distribution and leverages the mechanical integrity of the 3D-printed PLA scaffold and osteoconductive microenvironment for proliferation and differentiation offered by the silk fibroin and alginate hydrogel. The cell-laden gels loaded within 3D-printed scaffold showed improved proliferation and osteogenic activity of stem cells, which makes the system a promising bone substitute for regeneration or healing.