The identification and implementation of raw materials to replace fish meal (FM) or its major alternative, soybean meal (SBM), among other factors, is crucial for the sustainable growth of aquaculture. Narbonne vetch (Vicia narbonensis) meal (NVM) has previously been identified as a promising alternative raw material locally produced in Europe to replace SBM. Previous work has showed that 33% replacement of SBM by NVM treated with a commercially available phytase (Rovabio® PHY) does not compromise fish growth performance in a 63-day trial. Here, a deeper characterization of the potential use of NVM to replace SBM was performed to unveil any potential undesired physiological impact in rainbow trout (Oncorhynchus mykiss) juveniles with an initial weight of 38.04 ± 0.07 g. After a 63-day feeding trial, high (66%) SBM replacement by NVM (even when treated with Rovabio® PHY) had a negative impact on rainbow trout: decreasing the activity of alkaline proteases, trypsin, chymotrypsin, and α-amylase; inducing cell shrinkage in hepatocytes; and reducing plasma triglycerides and hepatic vitamin E (VE) levels. No biochemical alterations were observed in blood plasma glucose, cholesterol or redox enzymes, regardless of the % of SBM replacement and/or Rovabio® PHY treatment. In fish fed diets with 33% replacement of SBM by NVM (regardless of being treated with Rovabio® PHY or not), only a reduced content of plasma triglycerides, and a slight modification in the position of the nucleus in enterocytes (more intermediate) from the proximal intestine, were reported. Altered metabolism of both carbohydrates and VE was also confirmed at transcriptional level, possibly being related to the presence of non-starch polysaccharides (NSPs) in NVM. The present study identifies future strategies to improve the use of NVM as an alternative raw material to replace SBM, allowing greater sustainability, and a lower carbon footprint in European aquafeeds to be achieved.