The cultivation of two or more crops in association to each other is an ancient method of utilising agricultural area to get optimum crop productions. The increased cultivation of energy crops to fulfil energy requirements have led to the necessity of optimisation of bio productivity of the available land use, which should be carried out without compromising on the land quality and environmental conditions. Syn-Energy II is an Austrian national project, which focuses on the possibilities of synergetic expansion of agricultural biogas production. The field experiment results reveals that cultivation of intercrops for biogas production between the main crops enhances crop rotation yields, while it reduces erosion, greenhouse gas emissions and ground water pollution. Similarly synergetic calculations will be made for conservational soil cultivation and biological crop rotation systems. The project not only focuses on production of biogas for conventional use (heat and electricity production), but also biogas cleaning to natural gas quality (96 % methane content) which can be injected to the gas grid and its usage as an alternate fuel in the agricultural practice making a recycling loop (Niemetz and Kettl, 2012). The ecological assessment is carried out utilising Life Cycle Assessment (LCA) based methodology known as Sustainable Process Index (SPI) (Krotscheck and Narodoslawsky, 1996). A web based tool SPIonWeb (http://spionweb.tugraz.at/en/welcome) is used to calculate ecological footprint and dynamic modelling for biogas production scenarios, based on comprehensive energy and material flows from a variety of intercrop-systems. The process evaluation provides reliable information to figure out ecological hotspots for process optimisation (Kettl and Narodoslawsky, 2013).