Given a sequence of graphs
$G_n$ and a fixed graph H, denote by
$T(H, G_n)$ the number of monochromatic copies of the graph H in a uniformly random c-coloring of the vertices of
$G_n$. In this paper we study the joint distribution of a finite collection of monochromatic graph counts in networks with multiple layers (multiplex networks). Specifically, given a finite collection of graphs
$H_1, H_2, \ldots, H_d$ we derive the joint distribution of
$(T(H_1, G_n^{(1)}), T(H_2, G_n^{(2)}), \ldots, T(H_d, G_n^{(d)}))$, where
$\mathbf{G}_n = (G_n^{(1)}, G_n^{(2)}, \ldots, G_n^{(d)})$ is a collection of dense graphs on the same vertex set converging in the multiplex cut-metric. The limiting distribution is the sum of two independent components: a multivariate Gaussian and a sum of independent bivariate stochastic integrals. This extends previous results on the marginal convergence of monochromatic subgraphs in a sequence of graphs to the joint convergence of a finite collection of monochromatic subgraphs in a sequence of multiplex networks. Several applications and examples are discussed.