We consider the zero-average Gaussian free field on a certain class of finite $d$-regular graphs for fixed $d\geq 3$. This class includes $d$-regular expanders of large girth and typical realisations of random $d$-regular graphs. We show that the level set of the zero-average Gaussian free field above level $h$ exhibits a phase transition at level $h_\star$, which agrees with the critical value for level-set percolation of the Gaussian free field on the infinite $d$-regular tree. More precisely, we show that, with probability tending to one as the size of the finite graphs tends to infinity, the level set above level $h$ does not contain any connected component of larger than logarithmic size whenever $h>h_\star$, and on the contrary, whenever $h<h_\star$, a linear fraction of the vertices is contained in connected components of the level set above level $h$ having a size of at least a small fractional power of the total size of the graph. It remains open whether in the supercritical phase $h<h_\star$, as the size of the graphs tends to infinity, one observes the emergence of a (potentially unique) giant connected component of the level set above level $h$. The proofs in this article make use of results from the accompanying paper [AC1].