An integrated biorefinery (IBR) is a potential source of sustainable energy, biochemicals, and other high-value products. This biomass processing facility is developed by maximizing material and energy product (or by-product) exchanges between process units within an industrial plant. In the Philippines, vast amounts of agricultural residues (e.g., rice husk) remain to be tapped for bioenergy production. Aside from this, designing a viable and sustainable IBR is a challenging task due to the highly integrated nature of this system. In this work, a P-graph (process graph) based method is applied to generate optimal and near-optimal IBR configurations utilizing Philippine agricultural waste as feedstock whose objective is to maximize profitability. The P-graph framework was initially created to solve process network synthesis (PNS), but recently, researchers extended its use beyond the PNS domain (i.e., integrated systems). In addition, the P-graph software presents the results in a graphical interface, a distinct advantage compared to other optimization techniques. A case study utilizing waste from rice production in the Philippines is used to demonstrate the methodology. The resulting model shows the optimal configuration of the IBR and the maximum profit generated 1,208.17 USD/h. Local government units can use results from this work in creating policies to maximize bioenergy production and increase the revenue generation of farmers.