<p>An accurate description of low-density nuclear matter is crucial for explaining the physics of neutron star crusts. In the density range between approximately 0.01 fm⁻³ and 0.1 fm⁻³, matter transitions from neutron-rich nuclei to various higher-density pasta shapes, before ultimately reaching a uniform liquid. In this work, we introduce a variational Monte Carlo method based on a neural Pfaffian-Jastrow quantum state, which allows us to model the transition from the liquid phase to neutron-rich nuclei microscopically. At low densities, nuclear clusters dynamically emerge from the microscopic interactions among protons and neutrons, which we model based on pionless effective field theory. Our variational Monte Carlo approach represents a significant improvement over the state-of-the-art auxiliary-field diffusion Monte Carlo method, which is severely hindered by the fermion-sign problem in this low-density regime and cannot capture the onset of clusters. In addition to computing the energy per particle of symmetric nuclear matter and pure neutron matter, we analyze an intermediate isospin-asymmetry configuration to elucidate the formation of nuclear clusters. We also provide evidence that the presence of such nuclear clusters influences the amount of protons in the crust compared to protons in beta-equilibrated, neutrino-transparent matter.</p>