Chitosan-pectin hydrogels were prepared, and their rheological properties were assessed in order to select the best system to develop scaffolds by 3D printing. Hydrogels showed a weak gel behavior with shear thinning flow properties, caused by the physical interactions formed between both polysaccharides, as observed by FTIR analysis. Since systems with high concentration of pectin showed aggregations, the system composed of 2 wt% chitosan and 2 wt% pectin (CHI2PEC2) was selected for 3D printing. 3D printed scaffolds showed good shape accuracy, and SEM and XRD analyses revealed a homogeneous and amorphous structure. Moreover, scaffolds were stable and kept their shape and size after a cycle of compression sweeps. Their integrity was also maintained after immersion in PBS at 37 °C, showing a high swelling capacity, suitable for exudate absorption in wound healing applications.