Cysts of Globodera rostochiensis, a major constraint to potato production, are mainly distributed through soils. Waste soil, i.e. soil carried along with the harvested potato tubers from the field, can be treated by inundation, a disinfestation method creating an anaerobic condition of the soil. The anaerobiosis process can be accelerated by adding organic materials. The aims of this study were to evaluate the impact of inundation on survival of potato cyst nematodes and the effect of agricultural and industrial waste products on accelerating the anaerobiosis process. Experiments were conducted in closed 2-L containers filled with cyst-infested inundated soil. Cysts were placed in retrievable nylon mesh bags and buried in the soil. The effects of 6 treatments on cyst survival were studied over 8 weeks. Inundated containers were filled with (1) non-amended soil, (2) steamed potato peels, (3) fresh potato peels, (4) calcium sulphate, (5) a mixture of steamed potato peels and calcium sulphate and (6) leek. Non-amended, non-inundated soil in (7) closed and (8) open containers were included as controls. The viability of the cyst content was evaluated weekly by visual assessment and a trehalose-based method. To examine the infectivity of juveniles, sprouted tubers planted in closed containers were inoculated with cysts retrieved from the containers. After 4 weeks, the number of penetrated juveniles in the roots was determined. Quantification of volatile fatty acids (i.e., acetic, propionic, (iso) butyric, and (iso) valeric acid) in soil was done using gas chromatography coupled to a flame ionisation detector. Hydrogen sulphide, oxygen and carbon dioxide were also measured using gas chromatography. Inundation of non-amended soil caused 87% reduction in nematode survival after 8 weeks, while amending leek, steamed and fresh potato peels reduced the survival of G. rostochiensis in inundated conditions up to 99.9% after 4 weeks. Infectivity of juveniles was reduced after one week in inundated conditions compared with controls. However, no juveniles were observed in potato roots two weeks after inundation of amended soil. Visual assessment and the trehalose-based method showed the same survival results. In summary, application of agricultural waste amendments improved the effect of inundation on the survival of nematodes. Hereby, the depletion of oxygen and the formation of volatile fatty acids are involved in nematode suppression in soils amended with fresh and steamed potato peels, and leek. In addition, for leek the release of hydrogen sulphide, known to be toxic to nematodes, is probably also involved.