Abstract3D printed honeycomb structures constituted by neat polylactic acid (PLA) and conductive PLA (PLAc) with different cell sizes and thicknesses were manufactured through 3D printing technology based on material extrusion (MEX). These structures were arranged into bi‐layer honeycomb structures (BHS) for evaluation of the microwave absorbing properties at the X‐band (8.2–12.4 GHz) and Ku‐band (12.4–18 GHz) frequency ranges. The effects of cell size, sample thickness, layer thickness ratio and the nature of the top layer on the electromagnetic attenuation performance of BHS samples were investigated in terms of reflection loss (RL). The components geometric characteristics and the arrangement of the layers exerted great influence on the RL values and effective absorption bandwidth (EAB). Overall the bilayer structures with 5 mm total thickness presented the best EM response in terms of EAB and minimum RL, where the component with the larger cell size (7.7 mm), PLAc (1 mm) as the top layer and PLA (4 mm) as the bottom layer exhibited the best results with RL values of −41 dB and EAB of 9.5 GHz. The BHS system with 7.7 mm cell size was more efficient in Ku band frequency range, whereas that with 3.5 mm cell size gave better response in the X‐band frequency range. Therefore, RL values and EAB can be adjustable by modifying the building strategy of the printed parts, such as thickness of the sample, cell size and thickness distribution of the conductive and non‐conductive layers. The findings in this work show the importance of the building strategy to fabricate components with controllable BHS and improved properties for microwave absorption application.