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Abstract Implications of excess phosphorus (P) in waste streams obtained from soy‐based protein preparation processes on the environment and their potential utilization as P‐source are two significant understudied areas. Soybean‐based protein ingredients for food products retain comparatively enhanced functional properties and are cheaper than other plant‐based proteins. Soybean protein can be extracted and utilized as a food ingredient primarily by preparing soy protein concentrates (SPC) and soy protein isolates (SPI) from soybean meal/defatted soy flour (DSF). In a typical soybean processing facility, along with the soy products and soy‐protein preparations, the recovery of phosphorus as a coproduct will enhance the economic feasibility of the overall process as the recovered P can be used as fertilizer. In this study, the SPC and SPI were prepared from the DSF following widely used conventional protocols and P flow in these processes was tracked. In SPC production, ~59% of the total P was retained with SPC and ~34% was in the aqueous waste streams. For SPI process ~24% of total P was retained with SPI and ~59% went in the waste solid residue (~40%) and aqueous streams (~19%). About 80%–89% P removal from the waste aqueous streams was achieved by Ca‐phytate precipitation. This work demonstrated that in the process of SPC and SPI preparation the phosphorus from the waste aqueous streams can be precipitated out to avoid subsequent eutrophication and the waste solid residue with ~40% P can be reused as a P‐fertilizer as other applications of this residue are unspecified.