The modeling capabilities of simulating failure in composite materials have significantly matured in the last decades. However, there are still challenges in properly taking into account all relevant processes that lead to failure in bonded composite parts, such as rate-dependent plastic deformations, crack initiation, crack propagation and the interaction between transverse cracks and delaminations. Furthermore, the strength of a bonded composite part depends on the thermo-mechanical history as a result of different processing parameters, which must be incorporated for accurate numerical predictions. In this work, we present a modeling framework for simulating rate-dependent plasticity, fracture and fatigue in bonded thermoplastic composite parts. This framework is based on earlier work for simulating progressive failure in composite multidirectional laminates and extended to simulate bonded composite parts. It consists of a fatigue cohesive zone model that covers initiation and propagation. The effects of thermal residual stresses are taken into account with a cycle jump scheme, where explicit load cycles are used to compute local stress ratios, which determine the fatigue response of the material. In order to include the effect of plastic deformations in bonded parts, a mesoscopic transversely isotropic viscoplasticity model for unidirectional composites has been developed. The performance of the computational framework in simulating rate-dependent plasticity, fracture and fatigue in composite bonded parts is demonstrated with numerical examples. It will be shown that the framework can be used to predict the strength and life of bonded composite parts, taking into account manufacturing effects and thermo-mechanical history.