Part I (Aho-Mantila L. et al 2012 Nucl. Fusion 52 103006) presented a detailed analysis of outer divertor plasma conditions in low-density L-mode discharges in ASDEX Upgrade. In this paper, we analyse the local migration of carbon that originates from 13CH4 injected into these plasmas from the vertical outer target. Notable changes are observed in the local carbon deposition patterns when reversing the magnetic field in the experiments. Kinetic impurity-following simulations are performed using the 3D ERO code package with 2D background plasma solutions calculated with the SOLPS5.0 code package. The modelling shows that the measured changes are due to the changes in plasma collisionality, dissociation and ionization rates, and E × B drift of the impurities. These conditions affect the direction and rate of impurity migration inside and out of the divertor, having wider consequences on the global migration of impurities in a divertor tokamak. It is further shown that the migration pathways are largely determined by carbon ions and, hence, relevant for impurities in general. Neutral carbon and hydrocarbons are deposited only in the near vicinity of the injection, where they affect the local re-deposition efficiency. In this limited region, a perturbation of the local plasma conditions by the methane puff appears likely, yielding a significant uncertainty for interpreting the deposition efficiencies. The local deposition is largely influenced by the magnetic presheath electric field, the structure of which is the main uncertainty in the SOLPS5.0-ERO simulations.