Soil-borne diseases are the most significant crop protection problem in soil-based, low-input and especially organic glasshouse production systems in Europe. While chemical soil disinfestation has been the control method of choice in conventional farming systems, soil steaming has been the main strategy for the control of soil-borne diseases in organic production. Both methods are extremely expensive and have been increasingly restricted for environmental reasons by governments, and integrated and organic farming standard-setting bodies. The use of disease-tolerant varieties, grafting onto resistant rootstocks and chitin soil amendments were evaluated as potential replacements for soil steaming in organic and other low-input tomato production systems. When only Pyrenochaeta lycopersici and/or Meloidogyne spp. were present in soil, grafting and/or chitin soil amendment were found to be as effective in reducing root disease and/or increasing yield as soil steaming, but the efficacy of both treatments was reduced when Verticillum albo-atrum was also present in soil. No additive effects of combining grafting and chitin soil amendments could be detected. A more widespread use of grafting and/or chitin soil amendments may therefore allow significant reductions in the use of steam and chemical soil disinfestation in glasshouse crops. It will also allow integrated and organic farming standard-setting bodies to impose further restrictions on the use of soil disinfestation treatments.