This study proposes an evaluation of the Diffusive Gradients in Thin films (DGT) technique to assess the labile fraction of trace metals and metalloids in anaerobic digestates. Experiments were performed in presence and absence of air to determine whether maintaining anaerobic conditions is mandatory during DGT deployments. A theoretically expected linear accumulation profile was observed for Fe, Mn, Ni, Mo, and As(III) in a manure-derived digestate and for Mn in distillery waste-derived digestate, whereas Al and Cu were detected without a consistent trend over time. The DGT technique can thus be used to evaluate the labile fraction of some trace elements in these digestates. The labile fraction of some elements was shown to evolve over 72 h when deployments were performed in the presence of air. We thus strongly recommend to systematically perform time-series deployments to identify and consider only the elements with a linear accumulation trend and to maintain anaerobic conditions.