In this study, the development of innovative tooling and end-effector systems for the assembly of a multifunctional thermoplastic fuselage is presented. The increasing demand for cleaner and new aircraft requires utilising novel materials and technologies. Advanced thermoplastic composites provide an excellent material option thanks to their weldability, low density, low overall production cost, improved fracture toughness and recyclability. However, to fully appreciate their potentials, new manufacturing approaches and techniques are needed. Hence, this project develops three end-effector solutions to demonstrate the feasibility of assembling a full-scale multifunctional-integrated thermoplastic lower fuselage shell, including the integration of a fully equipped floor and cargo structure. The developed assembly solution comprises three individual yet well-integrated tooling systems that allow housing the skin and assembly; picking, placing and welding of the assembly parts, i.e. clips and stringers; and welding of frames and floor beam sub-assemblies. The process of developing these systems including the end-user requirements, technical challenges, tooling and end-effectors design and manufacturing process are detailed in this paper.