Bioenergy parks are typically composed of separate biomass-processing plants that have agreed to collaborate via material and energy product synergies to achieve more sustainable operations. The inability of one or more component plants to provide the agreed demand for a product will cause cascading disruptions in the entire network. The inoperability in a bioenergy plant can be caused by a reduction in available raw materials, internal equipment malfunctions, or delays in transporting goods within the supply chain. Despite the disruption, bioenergy parks can continue their operation by optimizing the network's allocation of the material streams. In this work, a P-graph method is developed to optimally adjust operations of a bioenergy park under capacity disruptions. This model considers the effects of deviating from the baseline demand by introducing a penalty rate. This penalty is a financial cost to be deducted from the bioenergy park's optimal economic potential as a result of not being able to meet contractual obligations. A bioenergy park case study is chosen to demonstrate the proposed methodology. Results show that there is about a three-fold further decrease in the optimal profit when penalty rates are applied in the model.