Sclerotinia rot is a disease caused by the fungus Sclerotinina sclerotiorum which affects a wide range of crops and causes major yield and economic losses. Crop rotation is an important strategy for minimising losses. A dynamic programming (DP) model was developed to study the trade-offs between state of the land, severity of sclerotinia and financial impacts as a result of different cropping decisions. Results showed that rotation and treatment against sclerotinia was financially justified yet permitted intensive yet sustainable production of susceptible food crops in the long-run. Allocation of even a small proportion of cropping decisions to break crops coupled with treatments in the rotation mitigated long-term build-up of sclerotia in land. However in the short-run, high proportions and high frequencies of cropping decisions need to be either allocated to break crops or treated-susceptible crops in order to avoid the disease and to generate profit. Results showed that DP methodology provides a useful framework to explore the trade-offs between crop rotation and growing high value susceptible crops in the long- and short-term in relation to plant diseases in arable agriculture that are at the heart of sustainable food production and land use.