We extend the covariance matrix description of atom–light quantum interfaces, originally developed for real and effective spin-1/2 atoms, to include ‘spin alignment’ degrees of freedom. This allows accurate modelling of optically probed spin-1 ensembles in arbitrary magnetic fields. We also include technical noise terms that are very common in experimental situations. These include magnetic field noise, variable atom number and the effect of magnetic field inhomogeneities. We demonstrate the validity of our extended model by comparing numerical simulations to a free–induction decay measurement of polarized 87Rb atoms in the f = 1 ground state. We qualitatively and quantitatively reproduce experimental results with no free parameters. The model can be easily extended to larger spin systems, and adapted to more complicated experimental situations.