Climate and environment of Gaia, mother Earth, are under multiple significant stresses. The increase in world population demands large increases in food production, but this must be reached by use of sustainable methods. Emission of climate gasses needs to be dramatically decreased, overall ecological footprints have to be diminished, and socioeconomy of rural areas has to be boosted. These aims are not easy to combine. However, the bio-economy and green solutions may provide mankind with tools of great value both to mitigate pollution and climate change and to adapt to future changes. It is clear that all forms of agriculture cause changes in balances and fluxes of pre-existing ecosystems, thereby limiting resiliency functions. Intensive agriculture in regions that are influenced by industrial pollution, with strong reduction of landscape structures and vast decoupling of energy and matter cycles, has caused stress and degradation of the production base; massive influence has also been exerted on neighbouring compartments. Average yields are probably close to 50 % of maximum yield many places, due to mismanagement of the crops during the production phase, or due to the inappropriate use of key resources. This relationship often leads to a mis-match between input of resources and process outputs, and creates pollution and unbalance in the landscape. Fertilizer runoff and salt accumulation occurs if water supply is in surplus or deficiency, due to soil compaction after use of large machines, and pollinating insects are suffering in regions with large monocultures and high pesticide inputs. These few examples show some of the dilemmas of using input factors in a way that does not fit with the overall conditions. Hence it will be as important as ever to develop new agricultural systems exploiting seasonal growth cycles through intercropping and the integration of mixed perennial crops to ensure permanent availability of plant fractions to be delivered to end users. The problem of degrading soils threatened by overuse, compaction, pollution and loss of biology can only be tackled by a cross disciplinary research approach addressing the entire spectrum of agricultural, environmental and socioeconomic functions of our agricultural systems. While efforts to demonstrate the benefit of site-specific management are relatively recent and have taken various approaches, they specifically refer to variable-rate applications of single inputs, e.g. seeds, fertilizers, chemicals. It is high time to deploy principles of precision agriculture for integrated crop management through combined variable inputs of irrigation water, fertilizers, composts and crop density to improve degrading land and on the other side produce valuable raw products for biorefineries and biobased industries In order to implement such novel production systems, for food and non-food products, the demonstration of land use changes, for biodiversity, for sufficient food and biomass production is essential, with emphasis on the diversity of species and varieties grown, harvested and converted to valuable products. Therefore this Research Topic combines studies demonstrating improved use of soil amendments, nutrients, as well as improved soil fertility for higher resilience against climate stress and recuperation of abandoned or contaminated soils for cropping and animal husbandry. Mixed cropping for high biomass production to create higher added value through the production and transformation of green biomass into novel products is presented as one of the solutions. Applied research for a sustainable and ecologically compatible land use aimed at sufficient food production is as important as ever. Adequate management plans have to be developed from modeling and implemented to increase soil life at the level of the local farm and the region. Growing biomass plants for biorefinery processes should lower production costs, avoid pollution of surface and groundwater, reduce pesticide residues, reduce a farmer’s overall risk, and increase both short- and long-term farm profitability. Such production systems are established amongst the authors of this Research Topic and will allow to obtain an integrated picture of the role of closed cycling loops for N, P and K, and water in an agricultural ecosystem. The next step will be to support decision-making using sustainability indicators and toolboxes as they have been developed for different agricultural systems. The availability of stable research networks of study sites across Europe will help to develop decision support systems applicable across a variety of domains for integrated food and non-food production in the EU, in regards to socio-economy, sustainability and ecology.