Abstract A major challenge at the interface of quantum gravity and cosmology is to explain the emergence of the large-scale structure of the Universe from Planck scale physics. In this letter, we extract the dynamics of scalar isotropic cosmological perturbations from full quantum gravity, as described by the causally complete Barrett-Crane group field theory model. From the perspective of the underlying quantum gravity theory, cosmological perturbations are represented as nearest-neighbor two-body entanglement of group field theory quanta. Their effective dynamics is obtained via mean-field methods and described relationally with respect to a causally coupled physical Lorentz frame. We quantitatively study these effective dynamical equations and show that at low energies they are perfectly consistent with those of General Relativity, while for trans-Planckian scales quantum effects become important. These results therefore not only provide crucial insights into the potentially purely quantum gravitational nature of cosmological perturbations, but also offer rich phenomenological implications for the physics of the early Universe.