A fundamental characteristic of composite materials is that the initial choice of fiber and matrix type together with the selected manufacturing process controls the properties of the final part. As the manufacturing process creates simultaneously the composite and the component, its influence on part quality must be considered. From a manufacturing point of view, considering equipment, energy costs and production rate, it is desirable to process the part at the lowest possible pressures and temperatures and with the shortest cycle times. The challenge consists of making the production process robust for economical manufacture by an improved understanding of the material/process/property relationships. This paper focuses on the computational and experimental analysis of fusion bonding in thermoplastic composites. The influence of the process parameters on the bond strength is investigated. The bond quality exhibits randomness, which may be problematic within an industrial context. Its origin has been explained through a simple probabilistic analysis. The process sequence is found to be a major source of this uncertainty, resulting in various thermal loading and bonding quality fluctuations. On this basis, three practical ways for quality improvement are proposed.