Structural potting is used to prepare honeycomb panels to fix metallic elements, typical in aircraft doors. In this paper, a full procedure for structural potting using robotic arms is presented for the first time. Automating this procedure requires the integration of, first, machining operations to remove the skin layers and prepare the potting points and, then, resin injection into the honeycomb cells. The paper describes the design, prototyping, and testing of specific end-effectors. Different end-effectors were explored to ensure efficient injection. The results obtained with the prototypes show that the potting quality is adequate to accomplish the required process checks for industrial manufacturing. The injection process time can be reduced by a factor greater than 3.5, together with the extra assets associated with the automation of complex tasks. Therefore, structural potting automation is demonstrated to be feasible with the end-effectors proposed for milling and injection, which are ready for use with conventional robotic arms in manufacturing lines.