Electromagnetic interference (EMI) significantly affects the performance and reliability of electronic devices. Although current metallic shielding materials are effective, they have drawbacks such as high density, limited flexibility, and poor corrosion resistance that limit their wider application in modern electronics. This study investigates the EMI shielding properties of 3D-printed conductive structures made from polylactic acid (PLA) infused with 0D carbon black (CB) and 1D carbon nanotube (CNT) fillers. This study demonstrates that CNT/PLA composites exhibit superior EMI shielding effectiveness (SE), achieving 43 dB at 10 GHz, compared to 22 dB for CB/PLA structures. Further, conductive coating of polyaniline (PANI) electrodeposition onto the CNT/PLA structures improves the SE to 54.5 dB at 10 GHz. This strategy allows fine control of PANI loading and relevant tuning of SE. Additionally, the 3D-printed PLA-based composites offer several advantages, including lightweight construction and enhanced corrosion resistance, positioning them as a sustainable alternative to traditional metal-based EMI shielding materials. These findings indicate that the SE of 3D-printed materials can be substantially improved through low-cost and straightforward PANI electrodeposition, enabling the production of customized EMI shielding materials with enhanced performance. This novel fabrication method offers promising potential for developing advanced shielding solutions in electronic devices.