In the present work, an ultrasonic, an induction, and a through transmission laser welding were compared to join carbon fibre reinforced polyetheretherketone (CF/PEEK) composites. The advantages and drawbacks of each process are discussed, as well as the material properties required to fit each process. CF/PEEK plates were consolidated at 395 °C with an unidirectional sequence and cross-stacking ply orientation. In some configurations, a polyetherimide (PEI) layer or substrate was used. The thermal, mechanical, and optical properties of the materials were measured to highlight the specific properties required for each process. The drying conditions were defined as 150 °C during at least 8 h for PEI and 24 h for CF/PEEK to avoid defects due to water. The optical transmission factor of PEI is above 40% which makes it suitable for through transmission laser welding. The thermal conductivity of CF/PEEK is at most 55 W·(m·K)⁻¹, which allows it to weld by induction without a metallic susceptor. Ultrasonic welding is the most versatile process as it does not necessitate any specific properties. Then, the mechanical resistance of the welds was measured by single lap shear. For CF/PEEK on CF/PEEK, the maximum lap shear strength (LSS) of 28.6 MPa was reached for a joint obtained by ultrasonic welding, while an induction one brought 17.6 MPa. The maximum LSS of 15.2 MPa was obtained for PEI on CF/PEEK assemblies by laser welding. Finally, interfacial resistances were correlated to the fracture modes through observations of the fractured surfaces. CF/PEEK on CF/PEEK joints resulted in mixed cohesive/adhesive failure at the interface and within the inner layers of both substrates. This study presents a guideline to select the suitable welding process when assembling composites for the aerospace industry.