We studied the interactions of lipid molecules (linoleic acid, glycerol trilinoleate and a complex mixture of wood extractives) with hydrophilic and hydrophobic surfaces (cellulose nanofibrils (CNFs) and polyethylene terephthalate (PET), respectively). The effect of lipoxygenase treatment to minimize the affinity of the lipids with the given surface was considered. Application of an electroacoustic sensing technique (QCM) allowed the monitoring of the kinetics of oxidation as well as dynamics of lipid deposition on CNF and PET. The effect of the lipoxygenase enzymes (LOX) was elucidated with regards to their ability to reduce the formation of soiling lipid layers. The results pointed to the fact that the rate of colloidal oxidation depended on the type of lipid substrate. The pretreatment of the lipids with LOX reduced substantially their affinity to the surfaces, especially PET. Surface plasmon resonance (SPR) sensograms confirmed the effect of oxidation in decreasing the extent of deposition on the hydrophilic CNF. QCM energy dissipation analyses revealed the possible presence of a loosely adsorbed lipid layer on the PET surface. The morphology of the deposits accumulated on the solids was determined by atomic force microscopy and indicated important changes upon lipid treatment with LOX. The results highlighted the benefit of enzyme as a biobased treatment to reduce hydrophobic interactions, thus providing a viable solution to the control of lipid deposition from aqueous media.