The Food-Energy-Water-Waste Nexus (FEWWN) represents the interconnections between food, energy, water, and waste production systems, and it has become a key research area. Enormous quantities of agricultural and organic wastes are produced throughout the FEWWN. Often, these wastes are not treated appropriately because their true costs are rarely quantified, and usually externalized to the environment. This shortcoming is addressed from a systems perspective fused with approaches from ecological economics. A regional bioenergy production model where bioenergy may be produced from ethanol and/or agricultural wastes is constructed. Ecosystem service valuation methods are integrated into the framework, allowing for bioenergy production systems to be designed to minimize ecological damage and/or maximize ecological restoration. These values are captured within a Green Gross Domestic Product (Green GDP) objective that values both energy produced and ecosystem service values lost/gained. System profit is another objective in the multi-objective model. The framework is applied to a bioenergy production system for the U.S. state of New York, which aims to produce 10% more bioenergy compared to its current levels. Net changes in Green GDP ranged from -$16.5 M/y to $90.6 M/y, and corresponding profits ranged from $7.2 M/y to -$74.5 M/y. Corn grain ethanol was the dominant source of bioenergy in solutions with higher profits, while ethanol from corn stover and bioelectricity generated from animal manure biogas contributed more bioenergy in solutions with increasing Green GDP. Results show that there is a trade-off between promoting natural capital/ecological health and financial profit. FEWWN system design should consider these trade-offs moving forward.