The need for protein is increasing exponentially as the human population grows, and leads to more waste from food processing industries. At the same time, the demand for fish is higher than ever and solutions are needed to address associated waste management issues because current disposal methods are environmentally damaging. While waste bones are considered low value as they are inedible, they are a potential feedstock for hydroxyapatite (HAP). HAP is a versatile mineral that has been used in biomedicine, environmental remediation, and catalysis. Existing literature methods for isolating HAP from waste are too hazardous for industrial use (e.g., calcination and/or concentrated base). To overcome this, we developed an industrially viable method to isolate collagen-containing HAP from Atlantic salmon (Salmo salar) waste using enzymes. The enzymatic treatment was optimized using Design of Experiments (analytical data and weight loss calculations as responses), resulting in a successful method requiring only 6 h, 15 μL g-1 Neutrase and 7.5 μL g-1 Lipozyme CALB L at 40 °C in tap water. To validate our method for industrial application, we successfully isolated >100 g of HAP by treating 15 salmon frames (backbones), and performed a simplified gate-to-gate life cycle analysis (LCA). This research is based off many of the 12 Green Chemistry Principles, including Principle 1, Principle 3, Principle 6, Principle 7, and Principle 12. Furthermore, it contributes to several of the United Nations (UN) Sustainable Development Goals (SDGs), such as UN SDG2, UN SDG 8, UN SDG11, UN SDG12, UN SDG13, and UN SDG14. In the future, to make this treatment even more sustainable, applications for the protein-containing hydrolysate could be developed so that this is truly a zero-waste process. For example, the hydrolysate could potentially be used as a liquid fertilizer because of the lack of acid/base used. Another way to make the enzymatic treatment greener would be to optimize the volume of water required for a successful reaction.