Despite the natural ability of bone repair, its limitations have led to advanced organic-inorganic-based biomimetic scaffolds and sustained drug release approaches. Particularly, dexamethasone (DEX), a widely used synthetic glucocorticoid, has been shown to increase the expression of bone-related genes during the osteogenesis process. This study aims to develop a hybrid 3D-printed scaffold for controlled delivery of dexamethasone. Hence, hybrid scaffolds were fabricated using a layer-by-layer 3D-printing of combined materials comprising polycaprolactone (PCL)-nanohydroxyapatite (nHA) composite, and DEX-loaded PCL microparticles embedded in the alginate-gelatin hydrogel. Encapsulation efficiency, loading capacity, and in vitro kinetics of DEX release were evaluated. Osteogenic differentiation of human endometrial mesenchymal stem cells (hEnMSCs) on DEX-loaded hybrid scaffolds was assessed by evaluating osteogenic gene expression levels (collagen I, osteonectin, RUNX2), alkaline phosphatase (ALP) activity, and scaffold mineralization. The hybrid scaffolds exhibited favorable morphology, mechanical-properties, biocompatibility, and biodegradability, enhancing osteogenesis of hEnMSCs. DEX-loaded PCL microparticles within hybrid scaffolds exhibited a controlled release pattern and promoted osteogenic differentiation during the sustained release period through a significant increase in osteonectin and COL1A1 expression. Also, increased mineralization was demonstrated by SEM and alizarin red staining. This study proposes that drug-loaded 3D-printed hybrid organic-inorganic nanocomposite scaffolds are promising for advanced bone tissue engineering applications.