The production of W and Z bosons in association with light or heavy flavour jets at the LHC is sensitive to the flavour content of the proton and provides an important test of perturbative QCD. In this contribution, measurements by the ATLAS experiment probing the charm and beauty content of the proton are presented. Inclusive and differential cross-sections of Z-boson production with at least one c-jet or one or two b-jets are measured for events in which the Z-boson decays into a pair of electrons or muons. Predictions from several Monte Carlo generators based on next-to-leading-order matrix elements interfaced with a parton-shower simulation, with different choices of flavour schemes for initial-state partons, are compared with the measured cross-sections. Moreover, measurements of inclusive, differential cross-sections for the production of missing transverse momentum plus jets are presented. The measurements are designed both to allow comparison to Standard Model predictions, and to be sensitive to potential extensions to the Standard Model, particularly those involving the production of Dark Matter particles.