The classical theory of continuum mechanics is formulated using partial differential equations (PDEs) that fail to describe structural discontinuities, such as cracks. This limitation motivated the development of peridynamics, reformulating the classical PDEs into integral-differential equations. In this theory, each material point interacts with its neighbours inside a characteristic length-scale through bond-interaction forces. However, while peridynamics can simulate complex multi-physics phenomena, its integration in the study of mechanical systems is still limited. This work presents a methodology that incorporates a peridynamics formulation into a planar multibody dynamics (MBD) formulation to allow the integration of flexible structures described by peridynamics into mechanical systems. A flexible body is described by a collection of point masses, in analogy with the meshless collocation scheme commonly used for peridynamics discretisations. Each point mass interacts with other point masses through nonlinear forces governed by a bond-based peridynamics (BBPD) formulation. The virtual bodies methodology enables the definition of kinematic joints connecting the flexible body with the neighbouring bodies. The implementation of the methodology proposed is illustrated using various mechanisms with different levels of complexity. Notched plates subjected to different loading conditions are compared with the results presented in the literature of the peridynamics field. The deformations of a flexible slider-crank mechanism compare well with the results obtained using a classical flexible MBD formulation. Additionally, three scenarios involving a rotating pendulum illustrate how the methodology proposed allows simulating impact scenarios. The results demonstrate how this methodology is capable to successfully simulate highly nonlinear phenomena, including crack propagation, in a multibody framework.