Nutrient recovery from organic green biomass after processing in a green biorefinery concept for the production of protein feed, biogas and fertilizer for organic farming was investigated. Mass balances in terms of wet weight, TS, VS, C, N, P, K and S were evaluated for processing red clover and clover grass into protein concentrate, press cake and brown juice according to the green biorefinery concept. Depending on the biomass, between 60 and 79% of C and between 52 and 63% of N, P and S in the fresh biomass were found in the press cake, while only 6–10% of C, 8–15% of N, but up to 27% of P and up to 26% of S were found in the brown juice. In contrast, less than 45% of K was transferred to the press cake and 19–31% of K ended up in the brown juice. Moreover, nutrient recovery in the digestate after anaerobic co-digestion of press cake and brown juice produced from clover grass in a pilot-scale trial was assessed in a bench-scale biogas reactor. The analysis of the digestate from the AD process revealed that 56% of the influent total-C was converted into biogas and that the share of ammonia-N of total-N was increased from 9.4 to 43% during the biogas process. Therefore, the proportion of plant available N was improved in the digestate. The digestate to be applied as organic fertilizer presented a C:N ratio of 7 and a nutrients N:P:K ratio of 4:1:12.