We analyze the partition function of three-dimensional quantum gravity on the twisted solid torus and the ensuing dual field theory. The setting is that of a non-perturbative model of three-dimensional quantum gravity, the Ponzano–Regge model, which is here reviewed in a self-contained manner and then used to compute quasi-local amplitudes for its boundary states. In this second paper of the series, we choose a particular class of boundary spin network states which impose Gibbons–Hawking–York boundary conditions to the partition function. The peculiarity of these states is to encode a two-dimensional quantum geometry peaked around a classical quadrangulation of the finite toroidal boundary. Thanks to the topological properties of three-dimensional gravity, the theory easily projects onto the boundary while crucially still keeping track of the topological properties of the bulk. This produces, at the non-perturbative level, a specific non-linear sigma-model on the boundary, akin to a Wess–Zumino–Novikov–Witten model, whose classical equations of motion can be used to reconstruct different bulk geometries: the expected classical one is accompanied by other “quantum” solutions. The classical regime of the sigma-model becomes reliable in the limit of large boundary spins, which coincides with the semi-classical limit of the boundary geometry. In a 1-loop approximation around the solutions to the classical equations of motion, we recover (with corrections due to the non-classical bulk geometries) results obtained in the past via perturbative quantum General Relativity and through the study of characters of the BMS 3 group. The exposition is meant to be completely self-contained.