One of the heaviest criticisms of (especially carnivorous) aquaculture, has been its use of marine ingredients. There has been a narrative that aquaculture has increased the pressure on marine resources. Although this has largely been debunked, and the global supply of marine ingredients from forage fish has declined since the 1990s, the efficiency of their use is still paramount. Fish In Fish Out ratios (FIFOs) and various derivatives have been developed over the last twenty years as an indicator of the efficient use of marine ingredients in aquaculture. Several drawbacks of the methods have been highlighted over that time, including focusing on the limiting ingredient (meal or oil) in the diet rather than the overall efficiency of their combined use, and the quality and application of both the “fish in” and “fish out”. The eFIFO method was developed that used an economic weighting to try to represent the qualitative value of the inputs (forage fish vs trimmings and meal vs oil), however it did not represent the nutritional content of either the fish input or output. Small, oily fish that have been the mainstay of the marine ingredients industry are extremely valuable as sources of micro-ingredients such as long-chain omega-3 fatty acids (LC n-3 FAs). It has been shown that retention of LC n-3 FAs from feed to whole salmon is around 50% but there may also be losses during the marine ingredient rendering process. This study sought to develop a simple metric based on the eFIFO principle that could measure the efficiency of nutrient transfer from marine raw materials (including forage fish and seafood processing by-products). A nutritional FIFO (nFIFO) was developed using a series of equations that followed the transfer of nutrients through materials linked to economic flows, so that the most limiting ingredients were identified, and that by-product utilisation was encouraged, meeting circular economy principles of zero waste and aligning closely with the guidelines set out in the EU Product Environmental Footprint Category Rules for Feed. To demonstrate the functionality of the tool, we applied the equations to literature data on LC n-3 FA content from forage fish species and derived marine ingredients as declared by the Norwegian salmon industry and for whole salmon from academic literature. We found that the tool worked well to highlight nutrient loss through the supply chain. We found losses at the rendering stage and at the feeding stage but the data on nutrient content was very variable within species and robust primary data should be used where possible. Using economic allocation much improved the nFIFO scores, serving the purpose of encouraging use of by-products from fisheries for marine ingredients over forage fish resources. The nFIFO tool can also be used for other key nutrients such as Vitamin D, B12, calcium, iron etc if the data is available for all relevant points in the production chain.