In the holographic approach to cosmology, cosmological observables are described in terms of correlators of a three-dimensional boundary quantum field theory. As a concrete model, we study the 3$d$ massless $SU(N)$ scalar matrix field theory. In this work, we focus on the renormalisation of the energy-momentum tensor 2-point function, which can be related to the CMB power spectra. Here we present a non-perturbative procedure to remove divergences resulting from the loss of translational invariance on the lattice, by imposing Ward identities. This will allow us to make predictions for the CMB power spectra in the regime where the dual QFT is non-perturbative.