The share of renewables is rising rapidly, especially in developed countries. Biogas production from purpose-grown phytomass is undergoing the fastest growth. The trend is linked to the production of vast amounts of fermentation residues. However, it has been repeatedly and independently reported that intensive or long-term application of fermentation residues into arable land changes soil structure, resulting in sharp degradation of its fertility. This is now compensated by more intense use of agrochemicals and additional agrotechnical operations such as biochar addition. However, the increased cost is beginning to threaten the economic sustainability of biogas production. Given the fact that the production of biogas from purpose-grown phytomass has become a strong pillar of the electricity grid, the threat to soil fertility may endanger its stability. The quality and quantity of soil organic matter (SOM) and in particular its stable organic fractions with ion-exchange properties (SOF) that determine soil fertility, or, more precisely, the transport of nutrients and their availability for plant growth, were investigated in detail. A novel, undemanding and quick method allowing the analysis and interpretation of SOM and its SOF was proposed and compared with conventional methods. It was confirmed that the adaptation of the new method enables farmers to better choose organic and mineral fertilizers and corresponding agronomic operations, so the soil can provide higher yields and an increased water retention capacity (up to 7%), which results in improved water retention during extreme rainfalls or droughts, altogether lowering the cost of purpose-grown phytomass, or, more precisely, improving the economy of biogas production. Abbreviations: SOM: Soil organic matter; SOF: Stable organic fractions of SOM with ion-exchange properties; WRC: Water retention capacity; ARC: Air retention capacity; TOC: Total organic carbon; CEC: Cation exchange capacity; HA: Humic acids; FA: Fulvic acids; NHSOM: Non-humified soil organic matter; PSOM: Primary soil organic matter; Cox: Oxidizable carbon.