The biorefinery using Ammonia Fiber Expansion (AFEX) pretreatment has been modeled for production of fuel ethanol from cellulosic biomass, but has yet to be fully integrated with cropping and animal production systems.  Integration of these systems will enable environmental and economic analysis of biomass production, possible secondary protein products, and fertilizer production along with ethanol fuel production.  A comparison is presented for several crop and animal simulation models including DAYCENT, the Integrated Farm System Model (IFSM), and IFARM.  Investigating alternative farm management strategies in conjunction with classical design for economic profitability can illuminate pathways that both generate wealth and enhance the environment for future biorefining systems.