Background: The composition and properties of a biomixture used in a biobed are decisive for pesticide sorption and degradation. This study was performed to investigate the capability of compost-based substrates in mixtures with citrus peel and vine branch straw and peat-based substrates in mixtures with soil and vine branch straw at different levels in order to degrade isoproturon and bentazone. Results: Dissipation and mineralisation rates of both pesticides were determined, and metabolic activity was followed as respiration. Compost-based substrates showed faster pesticide dissipation in the presence of lignocellulosic materials, as in garden compost and vine branch straw. The increasing content of vine branch straw in peat-based substrates does not seem to affect dissipation of the parent compounds. Low mineralisation rate was observed in all treatments. Conclusion: Higher pesticide degradation was observed in the lignocellulosic substrates, probably because of the development of lignin-degrading microorganisms which have shown to be robust and are able to degrade recalcitrant pesticides. © 2010 Society of Chemical Industry.