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 BMS3 group. The exposition is meant to be completely self-contained.