Ultralight mechanical resonators based on low-dimensional materials are well suited as exceptional transducers of minuscule forces or mass changes. However, the low dimensionality also provides a challenge to minimize resistive losses and heating. Here, we report on a novel approach that aims to combine different 2D materials to tackle this challenge. We fabricated a heterostructure mechanical resonator consisting of few layers of niobium diselenide (NbSe$_2$) encapsulated by two graphene sheets. The hybrid membrane shows high quality factors up to 245000 at low temperatures, comparable to the best few-layer graphene mechanical resonators. In contrast to few-layer graphene resonators, the device shows reduced electrical losses attributed to the lower resistivity of the NbSe$_2$ layer. The peculiar low temperature dependence of the intrinsic quality factor points to dissipation over two-level systems which in turn relax over the electronic system. Our high sensitivity readout is enabled by coupling the membrane to a superconducting cavity which allows for the integration of the hybrid mechanical resonator as a sensitive and low loss transducer in future quantum circuits.