In the present study, alginate-pectin (Al–P) hydrogel particles containing varied total gum concentrations (TGC) at a constant Al:P ratio of 80:20 were formed utilizing an innovative extrusion-based 3D food printing (3DFOODP) approach. The 3DFOODP conditions, namely, TGC (1.8, 2.0, and 2.2 wt%) and nozzle size (0.108, 0.159, and 0.210 mm) were investigated. The 3DFOODP approach was compared with the conventional bead formation method via a peristaltic pump. All Al–P printing inks exhibited a shear-thinning behavior. The increased apparent viscosity, loss and storage moduli were associated with the increase in the TGC. The size of the wet 3D-printed Al–P hydrogel particles ranged between 1.27 and 1.59 mm, which was smaller than that produced using the conventional method (1.44–1.79 mm). Freeze-dried Al–P particles showed a porous structure with reduced crystallinity. No chemical interaction was observed between alginate and pectin. This is the first report on generating Al–P-based beads using a 3DFOODP technique that can create delivery systems with high precision and flexibility.