The Industrial Revolution and intensification of agriculture have, in some cases, led to economic activities that profoundly influenced the ecosystem to the point where environmental stability and geographic political security are jeopardized. The uncertainty about oil reserves, rising energy prices and the threat of harmful climate change effects has intensified the search for alternative farming systems that reduce negative environmental impact. This study reports the ecological impact of conventional (CON), integrated (INT), organic (ORG) and biodynamic (BD) farming systems calculated from data collected in a field trial at Maribor, Slovenia, and interpreted using the SPIonExcel tool. This tool is a member of the ecological footprint family and describes the area necessary to embed a human activity sustainably into the ecosphere. Three-year results show a markedly reduced ecological footprint of the ORG and BD systems in production of wheat (Triticum aestivum L. ‘Antonius’) and spelt (Triticum spelta L. ‘Ebners rotkorn’), mainly due to the absence of external production factors. When yields were also considered, the ORG and BD systems again had a reduced overall footprint per product unit and increased ecological efficiency of production. Thus, ORG and BD farming systems present viable alternatives for reducing the impact of agriculture on environmental degradation and climate change. Nevertheless, room for improvement exists in the area of machinery use in all systems studied and yield improvement in the ORG farming system.