We present a novel approach to the construction of mock galaxy catalogues for large-scale structure analysis based on the distribution of dark matter halos obtained with effective bias models at the field level. We aim to produce mock galaxy catalogues capable of generating accurate covariance matrices for a number of cosmological probes that are expected to be measured in current and forthcoming galaxy redshift surveys (e.g. two- and three-point statistics). We use the bias assignment method (BAM) to model the statistics of halo distribution through a learning algorithm using a few detailed N-body simulations, and approximated gravity solvers based on Lagrangian perturbation theory. Using specific models of halo occupation distributions, we generate galaxy mocks with the expected number density and central-satellite fraction of emission-line galaxies, which are a key target of the DESI experiment. BAM generates mock catalogues with per cent accuracy in a number of summary statistics, such as the abundance, the two- and three-point statistics of halo distributions, both in real and redshift space. In particular, the mock galaxy catalogues display ∼3%−10% accuracy in the multipoles of the power spectrum up to scales of k∼0.4h−1Mpc. We show that covariance matrices of two- and three-point statistics obtained with BAM display a similar structure to the reference simulation. BAM offers an efficient way to produce mock halo catalogues with accurate two- and three-point statistics, and is able to generate a variety of multi-tracer catalogues with precise covariance matrices of several cosmological probes. We discuss future developments of the algorithm towards mock production in DESI and other galaxy-redshift surveys. (Abridged)