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The over-enrichment of phosphorus in waste streams can lead to eutrophication and oxygen limitations for aquatic life. To understand the release of phosphorus from a soybean processing facility, it is imperative to track the flow of phosphorus in different streams during the processing of soybeans. The objective of the study is to develop process simulation models to study the flow of phosphorus in the soy-biodiesel process and evaluate strategies to mitigate phosphorus release by recovering phosphorous from soapstock and wastewater. Since most of the P is found in soybean meal, the processing of which releases phosphorus, a third case of lecithin recovery was also studied to reduce the amount of phosphorous in soybean meal. It was observed that phosphorus can be economically recovered from the soapstock, as well as the wastewater stream, with an estimated operating cost of USD 1.65 and 3.62 per kg of phosphorous recovered, respectively. The phosphorus recovered from both streams can be potentially applied as fertilizer to more than 13,000 acres of corn or 96,000 acres of soybean, respectively. The lecithin recovery case was found to have the highest revenue, and it led to a 54% reduction in phosphorous during soybean meal processing.