This study introduces a 3D food printing approach to fabricate spherical starch beads with small sizes and high porosity for the first time. The results illustrated that 3D food printing could generate starch beads in different sizes depending on the nozzle diameter, printing pressure, and ink viscosity. The 3D-printed beads were characterized for their morphology, crystallinity, and textural properties, while the starch-based ink was analyzed for its rheological properties. A suitable printing was attained when viscosity was in the range of 1000–1200 Pa.s at a low shear rate (˂0.1 s−1). Among the starch concentrations (10–15%, w/w) investigated, 15% starch concentration provided the best control over the shape of the beads due to its high storage modulus (8947 Pa), indicating higher gel strength. At this condition, the starch beads revealed an average size of ~650 µm, which was significantly smaller than the beads produced with other starch concentrations (10 and 12.5%), and had a density of 0.23 g/cm3. However, at lower starch concentrations (10%), the beads were not able to retain their spherical shape, resulting in larger beads (812–3501 µm). Starch crystallinity decreased by gelatinization, and the starch beads exhibited a porous structure, as observed from their SEM images. Overall, 3D food printing can be an alternative approach to preparing porous beads for the delivery of bioactive compounds with high precision.