Green biomass from leguminous and gramineous forage crops, such as alfalfa and grass-clover, has been proposed as a potential new source of feed protein concentrates for non-ruminant livestock. However, the efficient separation of the protein fraction from the non-digestible cell components, primarily comprising cell walls (fiber) and starch, presents a significant technological challenge. Moreover, it is crucial to optimize the process to preserve the optimal nutritional value of the final product. This study comprehensively analyzed the non-digestible fiber content and composition across all biorefinery fractions using two different feedstocks: green biomass from alfalfa and grass-clover. The pilot scale refining process involved a combination of screw pressing, lactic acid fermentation, and protein separation via centrifugation. We observed variations in carbohydrate composition and abundance between alfalfa and grass-clover. The lactic acid fermentation led to a reduction in cellulose and total glucose content. Our findings indicate that the final protein concentrate still contains residual cell wall components, including lignin, indicating potential inefficiencies in the filtration, fermentation, and isolation steps. The presented analytical approach provides a valuable framework for optimizing processing conditions and tailoring enzyme cocktails for enhanced valorization of the by-products.