Imaging of the dust continuum emitted from disks around nearby protostars reveals diverse substructure. In recent years, theoretical efforts have been intensified to investigate how far the intrinsic dynamics of protoplanetary disks (PPDs) can lead to such features. Turbulence in the realm of non-ideal magnetohydrodynamics (MHD) is one candidate for explaining the generation of zonal flows which can lead to local dust enhancements. Adopting a radially varying cylindrical disk model, and considering combinations of vertical and azimuthal initial net flux, we perform 3D non-ideal MHD simulations aimed at studying self-organization induced by the Hall effect in turbulent PPDs. To this end, new modules have been incorporated into the NIRVANA-III and FARGO3D MHD codes. We moreover include dust grains, treated in the fluid approximation, in order to study their evolution subject to the emerging zonal flows. In the regime of a dominant Hall effect, we robustly obtain large-scale organized concentrations in the vertical magnetic field that remain stable for hundreds of orbits. For disks with vertical initial net flux alone, we confirm the presence of zonal flows and vortices that introduce regions of super-Keplerian gas flow. Including a moderately strong net-azimuthal magnetic flux can significantly alter the dynamics, partially preventing the self-organization of zonal flows. For plasma beta-parameters smaller than 50, large-scale, near-axisymmetric structures develop in the vertical magnetic flux. In all cases, we demonstrate that the emerging features are capable of accumulating dust grains for a range of Stokes numbers.