The aim of this study was to develop vitamin D3 (VD3) and iron (Fe) blended granules using Neusilin® US2 as an excipient. A central composite design of experiments was used for the continuous manufacturing process, considering VD3 and iron as independent variables and the bulk density, flow index, oil holding capacity, and color difference as response variables. The addition of VD3 had a significant effect on the powder flow properties. The X-ray diffraction and Scanning electron microscopy-energy dispersive X-ray analysis validated the presence of VD3 and Fe in the granules, whereas the variations in porosity and roughness were demonstrated by tomography and atomic force microscopy, respectively. The in vitro cellular uptake profile confirmed the absorption of VD3 in the breast cancer cell line MCF-7 with apparent apoptosis. These results could help in scaling up the process from laboratory to pilot scale in twin-screw granulation and boost the intervention of VitD3/iron deficiencies.