Additive Manufacturing has opened privileged roads towards rapid-realization of highly customized goods. The most spread AM technology is the Fused Deposition Modeling (FDM), that allows production of plastic prototypes and finished parts. Among these opportunities, the FDM technology offers the possibility of printing objects made up of different materials (Multi-Material-Deposition) to create objects characterized by local variations of compliance. This capability can be exploited to generate flexible joints that connect more rigid portions of the same object, enabling finite relative movement between portions of the object. In other words, it is possible to realize monolithic and joint-less structures that rely on the compliance of specifically designed zones to govern motion and forces transfer, i.e. the so called Compliant Mechanisms. This paper presents the design process of such a flexible junction, and how it is possible to embed a distributed sensor (i.e. an optical fiber) within it in order to measure the junction deformation and, then, read the relative movement of the two elements connected to it. The control of this type of systems, in fact, is always problematic because of the intrinsic 'uncertainty in the elasticity and mass density of the links', that can make open loop control systems prone to instability. Furthermore, the presented and discussed embedding technique can be also adopted to embed sensors in other types of applications.