Regenerative 3agriculture prioritizes soil health to build up organic soil carbon and nitrogen stocks while supporting the active and diverse soil biota that is a prerequisite for maintaining crop productivity and quality in sustainable food production. This study aimed at unravelling the impact of organic and inorganic soil maintenance systems in a ‘Red Jonaprince’ apple (Malus×domesticaBorkh.) orchard on soil microbiota biodiversity and soil physico-chemical properties. During our study, we compared seven floor management systems in terms of microbial community diversity. Fungal and bacterial communities on all taxonomic levels differed largely between systems that augmented organic matter (organic) and other tested inorganic regimes. The dominant phylum of the soil in all management systems wasAscomycota. The operational taxonomic units (OTUs) within theAscomycotawere largely identified as members ofSordariomycetes, followed byAgaricomycetes, and both dominated in organic systems versus inorganic. The most prominent phyla,Proteobacteria, accounted for 43% of all assigned bacteria OTUs.Gammaproteobacteria,Bacteroidia, andAlphaproteobacteriawere predominant in organic samples, whileAcidobacteriae,Verrucomicrobiae, andGemmatimonadeteswere more abundant in inorganic mulches.